The success Abrams and his team had with M:I:III was what got them the Trek gig.
Hmm. That would explain much of the extreme revisionism and gleeful junking of canon (as I understand it, the whole premise of the M:I film franchise was that Jim Phelps had gone bad; that, for me, would be reason enough not to see it even if I had only slightly more interest in Tom Cruise movies than I did in Mel Gibson movies).
You're completely off-base here. The film you're talking about was the first
M:I movie, which was directed by Brian DePalma and which Abrams had absolutely nothing to do with. Abrams only came onboard with the third film in the series, which came out a whole decade later.
Really, the first three M:I movies barely qualify as a series. Each is from a totally different director with a totally different approach, and each one basically ignores any continuity elements from the previous film, so beyond the continued use of the M:I title and the characters played by Tom Cruise and Ving Rhames, they're effectively three unrelated films that are more closely connected to their respective directors' overall bodies of work than they are to one another. It's only in the last two films (and the upcoming fifth film) that there's been any real continuity of story or style (because Abrams and Bad Robot have been kept on to produce the films due to the success of M:I:III). So your understandable objection, which I share, to the first film's treatment of Phelps has no bearing on any subsequent M:I film, and it certainly has nothing whatsoever to do with Mr. Jeffrey Jacob Abrams or any creative decision he's ever made in his entire life.