The one disadvantage is that there are really only maybe 5 or 6 top teams that are truly championship contenders in MoE. IF we had a full 30 car grid of just one class, imagine how easy it would be for a backmarker team to just 'give up' or not get any points? Would be quite boring for them, and there could be fast GT2 teams as well, and they'd be shooting for their own championship. People are generally pretty good while racing under blue flag... I don't think it really matters what car you have, you'll get some mistakes on behalf of the backmarkers no matter what car they use, even a GTR if it was all one-class.
The two class racing gives MoE some diversity and variety, rather than leaving the title to just a few top teams in only one class. There can still be plenty of normal GTR cars to go around (16+), so there certainly wouldn't be any shortage. But people should learn to drive in multi-class races, especially for endurance. Real endurance racing drivers have to deal with this all the time, and I don't see why you'd be so "scared" about it. If you can't drive with slower cars on the track (and vice versa), then you need to step away from the norm and try something proper for endurance racing.
A GT1 car could easily avoid an accident from a slow-going GT2 car, you have to be smart not to make any mistakes. And likewise, if there are stupid mistakes, penalties will be given. The majority of teams that have great racecraft have a growing interest in MoE this season, specifically for the 2-class racing. The more experienced teams would want to be in GT1, while other new entry-level teams would probably opt for GT2.
It isn't some mystery that there will be fast and slow cars on the track, I am sure everyone will be WELL aware of that. So I think your fear of accidents isn't unusual (happens all the time in real endu racing), but still kind of wimpy
In LFS GT (which had the FWD for the 2nd class), they had some nasty accidents between 2 classes, but it wasn't like every lap. They all looked to be easily avoidable, yet it is so easy to blame it on the slower car.