Love the article in general.
Not so sure I agree with the concept that AA was "detrimental" ... or that small sample isn't a factor in the 12 K/9 in his 19 AAA innings.  But, I appreciate the argument.
However, their are two key points you omit in your analysis in regards to Pineda's climb.
1) Mental makeup.  I don't pretend to know ANYTHING about this (or any other Mariner prospect - save a tiny crumb of insight regarding Ackley) in regards to mental makeup.  But, it *IS* a variable that good clubs have to consider and incorporate as part of their development program.
Pretty much every baseball player in the minors has largely been the best player (or near it) on every team they've ever played on.  The "default" state for todays pro-to-be athletes is that they've grown up being privileged and spoiled.  IMO, baseball has the slowest age-arc of every other pro sport in large part because baseball, moreso than the rest, DEMANDS a level of maturity that is extremely rare in those under age 25.  Talent can overcome "some" of that -- but how a 20 year old kid is HANDLED has a great deal to do with how he will eventually adapt to changing conditions - (and for most - losing the status of 'best player here').
Ian Snell would be my counter-example.  At age 20, Snell was doing pretty much what Pineda is doing -- trashing the minors at every stop.  Snell's final minor league composite?
62-22: 2.76-ERA; 0.6-HR; 2.4-BB; 8.7-K; 3.60-K/BB; 1.152-WHIP
Pineda is ahead of that pace: 30-11; 2.09; 0.4-HR; 2.0-BB; 8.6-K; 4.27-K/BB; 1.061-WHIP
But, the point here is that Snell possessed the "ability" from day one.  But, he didn't possess the "head" to deal with the realities of MLB hitters.  When he got to Pittsburgh, MLB hitters started hitting dingers instead of flyouts.  Snell got scared - and never has gotten over it. 
This is part of the reason I hesitate to accept that AA was "detrimental".  I see value in the simple proving of skill against higher caliber competition.  The "beneficial" part would've been, IF HE FALTERED.  If he falters against AA ... chances are MUCH high that there is a cause that can be found, adjusted, fixed, and success regained.  TEACHING a pitcher that he can "overcome adversity" ***BEFORE*** he reaches the majors is a major plus in my book. 
Even the supernatural players, (Lincecum), eventually hit some rough patches, where, against MLB hitters, they will suffer.  In May, Lincecum managed 4 CONSECUTIVE 5-walk games.  When a player has ZERO experience dealing with genuine struggles, "some" become completely lost.  It takes a MENTAL strength to deal with struggling with 30,000 fans in the stands and millions watching on TV (compared to 1,500 in the stands).
Of course, Lincecum gave up a total of 26 hits in 62 minor league innings.  When your "average" result is a 4-hitter, the minors aren't going to be competitive.  (Pineda, with 302 hits in 361 innings isn't even close to the Lincecum reality - (but not far from Snell).
But, "confirming" through production that a player is going to dominate a level doesn't require a full year at a level.  But, a month or two ... just to be thorough ... so you can at least give yourself a chance to mitigate the damage if/when a prospect DOES hit a wall ... I don't see that as detrimental.
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(2nd point to follow)

The second point that you missed is "impact on OTHER people".
I've said a number of times, one cannot establish orgaizational culture through words - you have to do so by ACTION.   Player development "must" take into account how decisions effect the players and coaches and future decisions AROUND a choice.  When the club elected to bring back Junior and Sweeney, it had an impact on all other DH potentials.  When they continued to trot the .500 OPS Griffey out day after day, it was an ACTION that effects the club's cred in regards to "entitlement".
There is "veteran entitlement" and "prospect entitlement".  Both are detrimental to organizational success.  Most players, with egos the size of Nebraska, are understandably annoyed when the 'uber-prospect' skips levels that they have to take in steps.  this doesn't mean you can NEVER promote aggressively, or skip steps -- it just means you have to be REAL careful it doesn't undermine your cred and development of everyone else.
If you promote Ackley (the #2) while he's hitting .700 - then every guy in AA hitting .800 and up has a LEGIMATE gripe of "why him and not me?"  Of course, after you PLAY with a guy for a month, it is possible to see the same things coaches and scouts see.  Players understand - "this guy is special" in a way fans cannot.  But, this REQUIRES for those other players to get a chance to see for themselves.
You send Pineda to Tacoma for a month or two, and the other pitchers THERE, who might have felt slighted if he had been jumped directly from AA to the Bigs will likely feel differently. 
The patience with Strasburg may not have helped HIS development.  But, even though it was only 55 innings, and he crushed the opposition ... it CERTAINLY helped create enthusiasm for two of Washington's minor league affiliates.  And it also was a hedge - a risk limit on a direct promotion.  "If" he stumbled at AAA, you can afford to be patient, because the Nats weren't going to compete in 2010 anyway.
And, of course, all those guys at AA and AAA who saw him, understand FIRST HAND, how special he is.  And they also have a subtle carrot -- if they want to play with him again - they BETTER work their buns off.
All that said - this doesn't mean step-by-step promotion is absolute.  It's not.  But, you better be REAL clear when you diverge from the norm that it can (and likely will) have consequences beyond the immediate decision.  The Braves plan was to start Heyward in AAA this year -- but he played his way into the starting lineup during ST - and he starred.
McCann skipped a level, too, IIRC.  (And the Braves traded away Saltamachia once they were locked in on McCann). 
Me?  I think the ENTIRE Seattle development machine is better served by the choice to move Pineda to Tacoma.  And if Lee is gone by the end of the month and Pineda replaces him, I'll view at as a near perfect balance of helping the team and helping the ORG.  A guy like Shell won't have to wonder - "why not me?" after a month of watching Pineda destroy the opposition.  He WILL have an idea of how much better he needs to be in order to get that call.
 

I remember Kirk Saarloos ... he had a habit of getting shelled his first outing at a new level, and then settling in and domination (until he hit the majors - which were simply beyond his talent threshold).  When you see a kid get crushed game 1 in A, A+, AA and AAA ... then when you promote him to the Bigs, you'll likely be more relaxed about an out-of-gate implosion.  ("The kid has nerves that take a start or two to get under control.")
Pineda, obviously has shown none of that.  Which, of course, is one (minor) point of taking the time to promote sequentially.  You get to see BEYOND the player - and get a read on the PERSON.  How does he transition into a new clubhouse?  Is he quiet and reserved and distant - or brash, cocky, arrogant?  And from 17-25 people are *becoming* who they eventually will be ... they aren't there yet.
So, a club has the added complication of dealing with a moving target.  That 20-year-old, who wants to party until 3:00am after every start may vanish by age 24.  And when you're planning on investing millions in a kid - EVERY bit of data is helpful.
The tricky part of managing - (not just in baseball, but in any business), is that the goal is to get the absolute most out of whatever talent your employees have.  But, on day one, you have no idea how to get the most out of THIS employee.  It takes time to learn what a kid's strengths and weaknesses are - and even longer to figure out what carrots and sticks he will most readily respond to. 
If Branyan is going to hit .900 batting anywhere but 4th - but is going to be unhappy and nervous, if you DO hit him cleanup, you hit him 2nd or 3rd ... keep him happy, and be happy that you're maximizing HIS productivity - (even if there is a nominal cost to the team).  Because, unhappy players rarely produce at their peak. 
In OOTP (the sim game), you just promote your best guys by the numbers and see the results.  In the real world - you HAVE to remember that these are human beings with human frailties, (and especially egos).  When your development train has been parked in the station for a decade, it may take awhile to get it going.  But, the potential rewards are huge.