I agree that that’s the history as presented. But what’s presented is a pretty short capsule summary of thousands of years. I think there’s plenty of room for Rajaat to have changed plans between setting up the first preserver school and starting killing preservers, or to have had multiple plans running before eventually settling on the Champions/Cleansing Wars one.
I think he probably didn’t have, or at least hadn’t fully committed to even if he had it in mind as an option, the Champions/Cleansing Wars plan when he started teaching. He wanted to undo the Rebirth by then, sure, but he might have originally wanted to do that by direct magic - “reverse the polarity” on the Pristine Tower and use it to undo the changes it had made, or transform life directly back to its Blue Age forms and gate in tons of water from the Plane of Water. (The latter seems to be what he’s actually doing when briefly free in Cerulean Storm - in addition to all the water, weird coral plants appear.)
But he learned that the Pristine Tower, at least as is*, couldn’t simply undo what it had done, and his power wasn’t (or wasn’t yet … He kept researching the Inner Planes during the Cleansing Wars) sufficient to do the second one, and the preservers he trained couldn’t help much. They could grow some grass (rejuvenate spell) but what good was that in the Green Age?
And so he went to Plan C (maybe with an intent to use the gathering of vast amounts of life energy through Champions’ dragon magic to fuel his real plan?) and he was set on his evil path.
*I think it would be interesting if (and this isn’t entirely original to me, I think someone suggested something similar ages ago on the WOTC forums when those existed) there was some remaining link between the Pristine Tower and the Rebirth Races it created, a link Rajaat exploited somehow, but one that also limited what he could do. That’s maybe why he couldn’t teach, or couldn’t do as well teaching, halflings magic; they didn’t have that link, since they were never remade by the Tower.
And so Rajaat ultimately decided that to get the full power of the Pristine Tower back, he had to kill off the Rebirth Races - not just because they didn’t exist in the Blue Age, but because some of the Tower’s energy was still “out there”, “committed”.
Or maybe it wasn’t magic he couldn’t teach, but the dragon metamorphosis (and/or Champion transformation, in the version where that’s a separate thing). Maybe the physical metamorphosis of an advanced being needs a Rebirth Race; it’s a hack built atop changes already made by the Tower, and a halfling or kreen has nothing to add that hack to. (This works better in the older material where half-elves could be dragons as Dragon Kings says, rather than human-only as Defilers and Preservers says.)