If Bastion did realize the person he fell for was a mutant, he'd be so resentful and can't decide if he loves or pities or hates them, wants to kill them, remove their powers, put a collar on them, infect them with Sentinel Code. He's the one mutant he doesn't want to kill, but is adamant on inhibiting their powers with a collar or other means.
He views them being a Mutant as them being cursed, so he wants to inhibit it to "save" them from themselves and/or just wants to control them. He resents them for making him feel this way and controlling their powers is one way to "punish" them for that.
And to ensure that they have a proper future, he makes sure via Mr. Sinister that any children Darling can have are all non-mutants. The man has massive mommy issues so that is absolutely gonna get projected onto a fem Darling, especially if their personality reminds him of his mom. Just like how she was only trying to protect him, he's gonna protect his Darling and make sure they go down the path HE knows is best for them.
That said, he'll be a bastard to them if they keep trying to resist him: berating them for being too stupid, stubborn, brainwashed by the likes of the X-Men and Magneto's cult, blaming them for making him feel this way despite what they are--what HE is.
And then he'll apologize for getting too "heated." Of course you're going to fight him and fight the new stage of mankind's evolution. People are resistant to change, he knows that. But once his future comes to the world, you'll see that it really is what's best and know where your place is: right there, underneath him with a Mutant collar around your neck. You'll be happy when you finally understand that.