What confuses me more is why they are sacrificed to do so to begin with

It's never explained, but I like to think it's because you can create more life with an entire body than with a drop of blood.

But it could for plot convenience, as they sacrifice themselves to create us and at the end they wanna kill us any way, gives a twist (the facehuggers/aliens are not the main bad guy) and mistery to their true intentions. We should be happy for the characters finding an engineer, only to be backstabbed that he's a bad guy.

why they end up wanting to kill them at the end

Haven't watched the movie in a while, but I always assumed it's because they see themselves as gods and us (humans) as peasants, they can do what they want, but who knows. I always assumed this would be explained in another movie.

There's a deleted scene in which Weyland talks about him and the engineers being gods because they can create life from nothing, but the engineer goes ham anyways.

Maybe they just created life to terraform planets and when humans are not needed anymore they would exterminate them.