Wanting to be loved and desired for herself and not as a baby machine/mother isn't out of line. Amelia is more than her uterus.
If Linc had said from the beginning that he wasn't sure of the relationship but let's try to make it work for the baby, then I'd have no problem with him pulling back with paternity in doubt.
But he didn't. He went all in and convinced Amelia that he loved her. That he wanted her. That they were good together. And for her to find out that that those things aren't actually true, Linc is really only with her because of the baby and now he's potentially out is incredibly painful.
Amelia didn't do anything wrong. Going from one partner to another isn't a bad thing. Birth control failures happen and have to be dealt with. She was honest in telling Linc about the pregnancy and at that time had no reason to believe that paternity could be an issue. And when paternity became an issue, she was honest. Amelia could have just as easily kept her mouth shut. But she instead she faced up to the problem.
Only to find out the person who said they loved her didn't really mean it. He's not with her for herself, he's potentially with her provided she's really carrying his baby. Amelia is reduced (again! already been through this with Owen!) to her ability to provide children. Which sucks!
Not to mention, at the end of the day when the paternity is figured out Amelia is going to be stuck co-parenting with either Linc or Owen. For at least the next 18 years she's either going to have to deal with the guy who has apparently lied about loving her or the guy who's life she's going to have to blow up and will probably lose his s**t again when she does so.