Without having been there, if the examples in the OP were the only offenses, they wouldn't have even registered on my radar. Not even a little. I can't call them rude for that. If they were showy about their affection, calling attention to it, or paying no attention to the conversation, that's another matter, but sitting close to one another and a little bit of non-sexual touching? That seems to be too picky.
I had someone at church once approach me and tell me that I was being inappropriate with my husband during bible study because I had my arm tucked into his. We asked the pastor, and he assured us we were fine, but I never wanted to speak to that woman again. I felt horrifically judged for simply sitting closer to my husband so we could share a hymnal.
It's not wrong for your mother to disapprove of their behavior and not want it in her own home, but if it was really as innocuous as it appears to me, don't be surprised if your friend no longer wants to come around and be judged for liking her boyfriend...