You are absolutely right about that (and Astrid also brings that up when they talk about it at the end of Guide Route, that it's an immoral thing to do), so it's definitely a tough choice to make.
I kinda wanted things to be morally gray like that; is it better to have people suffer for years and years until they figure something out for themselves, or is it better to help them along? Also, do we have the right to help people who don't ask for help?
Questions like that are also there because for The Guide the answers are simple, but for Astrid they're hard, so in a way she does lose part of her humanity when she decides to join him, even if she has good intentions. And while she thinks that it's the better out of two bad choices, we'll have to wait and see if it turns out to be the right thing to do in the end. :)
There's also the fact that The Guide offers to restore her memory, which definitely influences her decision. Like ordinary humans, she isn't perfect, and I do believe that if he didn't offer that then maybe she wouldn't have given in to him.