We just recently rehomed some guineas that we had. They started attacking our big rooster, but they were in the lot with the chickens at the time. We could only let them out to roam in the yard if we could supervise because they always wanted to roam into neighbors' yards. The neighbors said they didn't mind, but we didn't want to take the chance of them messing up someone's garden, so we gave them away to a guy with 30 acres for them to roam around on.
If your guineas free range and aren't in the lot with the chickens, then I don't think they'll intentionally seek out your chickens just to bother them, but if you keep them penned in together, it's very likely that they'll eventually start going after your rooster. I think it's only the male guineas that do this, so if you just have guinea hens it shouldn't be a problem.
As for your big rooster flying over the fence to attack the other one, I've seen 2 roosters try to fight (and be somewhat successful at it) through a wire fence, so it's possible. The pet roo I had at the time, Copper, managed to get pretty beaten up from that ordeal. I never expected that another rooster would attack him from outside the fence, and if he could've flown over the fence and into the lot, he probably would have.
This particular problem could probably easily be taken care of by throwing some pvc wire netting over the top of the run now that I think about it. It's like $11 for a 150' roll at the Lowe's around here.
