There were probably a lot more guns that were blued, either rust, charcoal, or temper than were browned. Even some original texts that talk of browning could be stating a rust blue finish. As was said the Hawken brothers blued their rifle barrels and many other contemporary builders did the same.
If you look into the research that has been done on early American longrifles you will find a general consensus that many of these guns were blued originally, or simply left in the white. Over time these surfaces patina and the resultant brown color has fooled many people into thinking that that is the original finish.
I don't know whether I would agree that one finish is more durable than the next (rust blue vs. brown). My experience has been that they both hold up exceptionally well, far better than modern hot dip blues. Both bite into the steel during the process rather than just lying on the surface. Also, when you consider that you can have a very fine rust blue or brown, or a relatively course one you have two different conditions that will wear differently.
Basically I would use whichever one makes you happy, both can be very attractive/durable when done correctly and both are historical finishes.