Umm, what do you think an artificial intelligence sentinel building factory is for exactly? It's meant to output thousands of Sentinels as fast possible, and you don't build thousands of Sentinels if you don't plan to use them to exterminate mutants off the face of the Earth. Also, every possible future Moira has explored the humans built Mother Mold, developed Nimrod, and perpetuated mass genocide on the mutant race in every single possible future she has tried so far.
Sure when she sided with Apocalypse they gave as good as they got and decimated the human race to some extent as well, but that's honestly as far as they got, and even in that future the Sentinel factory kept building better and better Sentinels which eventually enslaved humanity while on their course to exterminate mutants.