I think the OP is looking at this from an unhelpful angle. She seems to be asking the question, should we get married or should we live together as husband and wife without the benefit of marriage? She seems to assume that it’s either one or the other between those options. First of all, we all know that having extra-marital sexual relations is sinful, so that option ought to be taken off the table completely. So, what are her reasonable options? She can marry the man and hope that things don’t go to heck in a handbasket. There’s nothing morally wrong with this choice but it probably isn’t the most prudent. She can work with her boyfriend, their families, their counselors, and the priest to identify and assemble all their available resources and attempt to come up with a long-term plan that will enable them to reach a goal of living securely as a married couple with a child and work toward that goal so that they can get married in the near future. Or, she can determine that due to the nature of her disability, she is not currently in a position to plan for marital life and her primary focus should be to work on co-parenting this child.
I think going to a priest for advice is an excellent idea, not because the priest is going to find some sort of moral loophole in natural law, but because a priest would be able to talk to them and find out enough details about the situation in order to guide them to a realistic and moral solution to their problem.