One correction:
You didn't know about the trolls.
The raising of the trolls, summoning of the Varrangoin, killing and raising the 3 natives, and summoning the spectre, all occurred during Ke'Sha and Allakhain little trip to the woods. So they left 4 (with their quasits) and return 12. With any alteration (I thought of the Mask, but Limited wish is far superior to that) they can be mixed with the other monsters (extra troll-like, ogres, orcs, evil humanoids maybe drow-like and so on), and hopefully throw off suspicion enough to not even trigger the need to check his words.
It make sense he would be asked if he was around the village, he can either say he saw it from a far and it was quiet, and try to keep vague,
or say the plain truth that he was going to recruit undead monsters, got near the village, saw a mixed group of undead trolls and other creatures in the woods, did his best to control them, and managed to control some of them. (the mixture can explain other races if that's what the limited wish will do, and so far all is truth - just with bad context).
Maybe since people are reluctant to speak with him, and all of this is true and may let their imagination fill the gaps that he don't know about the kidnapped villagers and if the trolls and the others where in the village or not, but there is a good chance more monsters were there (because he says he controlled only some) and they might have been those who made the kidnap/killing/devouring/burn-to-ash/... of the natives, they will let it slide.
Of course if he will be farther investigated, when we as players know off-game that he did it, and push harder to that suspicion, eventually I won't be able to find reassuring excuses that are not plain lies and there will probably be a clash.
If the party still suspects him, not regarding the native specifically, even though he casted 'unfailing endurance' and was polite lately to everyone, suffering Hygiene jokes even that they are completely incorrect, Ke'Sha can promise (while grinning evilly) to prefer using Resurrection on party members before turning to raising them as undead. Given that he memorize it.
[JOKE]
To Ke'Sha defense, he didn't have a choice. The spells require humanoids and they are usually harder to find in dungeons he lately been to. Also, if he could make these undead without killing the native, selling their souls, or ruining their future, he would gladly do it. But he didn't write the rules, and they state all of the above is part of the process.
[/JOKE]