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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)