It's all about the timeline.
10,000 to 20,000 years ago North America would have been closer in climate and general flora/fauna to northern Europe (Scandinavia) or Siberia. In the modern era, say since 6,000 years ago or so, there's been slow long-term warming that has slowly been pushing arctic species further north.
Then the white man came.
Indians weren't the forest stewards they are often depicted as, since they primarily managed by fire. There are accounts from early in the colonization of New England of forests with enough space to "drive a coach between tree trunks." What forest do you know of that has that kind of absence of undergrowth?
Before logging, though, there's no question the Smokies would have had cooler stream temperatures much lower down, even without factoring in longterm warming. I would estimate that brook trout probably reached the Townsend area even as late as the 1850s, especially in winter. With logging came siltation (a big deal) and exposure to more sunlight (also a big deal), and thus warming. Roads along the streams even today, in a period of reforestation, prevent the canopy from cooling the water as much as it might (but we have it much better than they did 75 years ago, thus the reintroduction success of brookies in lower elevations like Lynn Camp Prong. That would not have been possible without a mature tree canopy.
So to answer your question, I suspect brook trout would have terminated in the flat bottoms around Townsend and given way first to species like horny headed creek chub and then further down to redhorse sucker, smallmouth bass, and eventually longnose gar. I'm not sure if largemouth bass would have been native to that water or not (though Indians certainly might have done some stocking).
Just an interesting historical note: in the Toccoa River in North Georgia, the Catoosa Indians built large fish weirs, big V-shaped things that were then maintained by the Cherokee. Today you can still see the foundations, and driftboat guides have cut holes in them to get through at low water. Those Indians were fishing primarily for redhorse suckers, I'm told. If you've never had redhorse, you're missing out; they are actually delicious (but they have a lot of weird floating bones).