I agree that while she was in London she certainly didn't want him involved with her pregnancy -- as she explicitly tells him in the schoolroom scene. I would even say that it was "high-handed" of her. But once she returns to Portwenn, I suspect it wouldn't have taken much effort on DM's part to persuade her to let him be of some help and support in her pregnancy and afterwards. I don't think she intended to press him for this in any way, but if things had started off on the right foot, I think she would have allowed him as much involvement as he wanted.
Once she leaped to the conclusion that another woman was in his life, though, I can see her refusing to deal with that situation by trying to steer clear of him, and any offers of help. Of course, the leaping to conclusions was foolish, but I think her feelings were more complex than just wishing to shut him out.
Yes, I see her (with her bags in the taxi) as hoping that DM will take her in, miraculously prove he's happy about the prospect of a child and life will be rosie. But as soon as she sees Edith her hopes are dashed and then DM acts, well like DM and all the past disappointments are brought back to her and she realises the rosie picture she'd built up about DM and the future is never to be.
I agree that the "anyway" tacked onto the thank you was unnecessarily mean but shows she must really hate/resent him at that time for not being her knight in shining armour.