No, it was the head of Gulf + Western, Martin Davis, who killed that idea. Here's an excerpt from this article about the development of Star Trek VI:
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Ultimately, when Martin Davis (the head of Gulf + Western at the time) was told that production was ready to begin on a sixth Star Trek film, he asked if Shatner and Nimoy were happy with the script. When he was told that they essentially had cameos, Davis reportedly hit the roof, and that's what caused the sudden push to do a Classic Trek movie.
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To further support this statement, George Takei had leaked it out to the fans at Star Trek conventions that Harve Bennett had developed the Starfleet Academy script with a younger cast in mind for the Original Series characters, with Shatner and Nimoy in bridging cameos. Reportedly it had something to do with a death and it tied in with Kirk's Academy days, where he met a Spock who had been estranged from Sarek and a Leonard McCoy, an older cadet, who went into the Academy after his father's death (at least that's what I remember, though I could be wrong in some areas). It was to have been prepared for the 25th anniversary of Star Trek's premiere. The fans didn't like that idea one bit and said so to Paramount Pictures, demanding that a final film with the complete Original Series cast be prepared instead.
I had the opportunity to meet Walter Koenig (Chekov) in 1990, and he expressed his displeasure over certain aspects of both the Star Trek V script and the Starfleet Academy script and wanted to do a final film with the original cast as a proper sendoff. He and I agreed that while his turn as "Captain Chekov" was refreshing in ST V, it would have turned into a bit of bad comic timing if in ST VI they said "Captain to the bridge", and all seven of the original cast hit the bridge at one time.
Of course, by the time of "Trials and Tribble-ations" (DS9), we learned that McCoy went to Ole Miss prior to the Academy (and for that, Mississippi State fans are still in an uproar! It's a college rivalry thing, y'know).
Ironically, since then there have been numerous novels, young adult novels, and comics devoted to the Original Series cast, the TNG cast, Janeway from Voyager, and other people at Starfleet Academy, as well as the CD-ROM game of the same name. So would a Starfleet Academy movie have worked? We may never know.
