Coloration is a pretty tough thing to judge any fish by in any event.
Here's a large brookie which was unquestionably stocked, as my cousin caught it in the Norfork River in Arkansas:
As you can see it was quite colored up; those fish make a spawning run in the winter time and tend to cluster in certain places around the Dam. I once caught three brookies over 12" in three casts (on an olive Matuka) right at Norfork Dam.
Supposedly your brighter fish with better coloration are that way because of better nutrition. I have heard that fish showing both orange/pink flesh and orange outside colors are eating foods high in beta carotene, especially crustaceans. One reason the browns in Arkansas are always so colorful is the high scud/sowbug content over there.
But I've definitely seen examples of unquestionably wild fish from our eastern forests which were dark and murky looking, despite having good nutrition and size. I think this is natural selection at work: your brighter fish don't last as long.
One more thing: I have been told by qualified biologists, including from the NPS, that the only way to tell Southern Appalachian (native) brookies from their northern brothers is via a complex genetic study. Evidently both fish are so closely related that the individual range of variation for a given fish's "look" overlaps to the point that you can't tell them apart by looking, even if you do things like gill raker counts. This is why it's been very difficult to isolate Southern from Northern fish pretty much across the Southeast (where northern strains were stocked in many places). Thus I'm a little skeptical about calling the fish I catch either "northern" or "southern" strains, no matter where I catch them.