Ainz is heartless against enemies, not his people. If they officially become his people, he'll be as nice as any ruler in their world, which isn't really nice but still not genocidal. Also, the alternative is a brutal death, so... easy choice.

How the heck can they deduce it was a time stop ability? The more probable deduction is "Ainz was too fast" or "Ainz used a mind trick spell" versus him actually stopping time, which is kind of ridiculous btw.