First, I don't think it is a good idea to train your girlfriend, and it would probably be best for your relationship if you find her a coach (rare exceptions apply here).
I would try the regular squat making the grip accommodation that you did. The amount of discomfort will probably diminish over time. Still, I would not expect much improvement in ROM, and she may just have to squat with an asymmetric grip (I have had plenty of people with shoulder issues use this strategy). If the grip issue is causing significant discomfort to the point where you think she may stop wanting to train switch to high bar or a safety squat bar. Rows or a form of pulldowns (if the overhead ROM is not pissing things off) will be a great exercise to introduce when the time comes to decrease deadlift frequency.