We could use more detail about the roof framing for confident answers, but here are some thoughts.
A house that old has a few things going for it. One is heavy, old-growth lumber. Another is heavy roof decking (probably 7/8" thick solid wood boards 8-14" wide). Yet another is beefy nails. For that reason, the roof as a system is probably still ok.
Yes, I would've headed off those rafters. There's stress on them in one direction or another, depending on overall framing design, and that should be managed to avoid sagging, etc.
No, roofers don't necessarily know (or care). They're in a square-foot-per-hour business with thin margins. Any delay could cost them their entire profit margin. Therefore, delays and distractions are minimized. This might be a reason to hire a carpenter who knows some roofing rather than the inverse for this job.
Many rafters are still "only 2x4s", even with engineered trusses of considerable span. They do the job perfectly well when used properly. My guess is that your attic has 1x4 webbing in several locations on each rafter reducing local spans.
At this point I'd get a good look into the attic and take a walk on the roof. I'd want to know the exact framing strategy and what the deck feels like under load. There may be repair to be done.
Update after new information... The solution here is fairly simple, I think. Open the drywall and install double 2x4 headers between the adjacent rafters using suitable joist hangers. Just toenailing the headers in place doesn't provide enough shear support, in my opinion. It might be ok if 4 nails can be driven from the outside face of the rafters, though. Still, hangers are dirt cheap.