Yes. The person who went back to the room should have to go to the back of the line when they return, just like everyone else. I would have. Sure, it may seem unreasonable when it's one person, but what if it were 5 people (joining one person who had been waiting in line)? What if that group of 5 people consisted of both scooters (now leapfrogging the woman who had been waiting and causing her to wait for another additional bus)? It's a slippery slope.
The fairest and most reasonable way to approach the situation is for everyone to wait on line in the order that they get to the bus stop prepared to get on the bus. If the party wanted to travel together, they should have all moved to the back of the line.
The OPer's brother in law cut in front of that belligerent woman causing her to have to wait for another bus (which, lately, on Disney schedules could be lengthy) - I don't blame her for being aggravated. She handled the situation about as badly as she could and in a completely unacceptable manner, but I still think she had a good reason to be unhappy with the situation.
So even though we told her ahead of time that there was a second scooter returning AND she said it was all right, you still don't blame her for becoming aggravated when my brother-in-law returned? I completely understand what you're truing to say, but she was not only being irrational but hypocritical.