This is a topic that I feel pretty strongly about. Theoretically, if it was possible to eliminate all brown trout (and rainbows) from streams in PA and bring back brook trout with population sizes that they once had, I'd be all for it no doubt. I dream of being able to fish the north central PA area back when it was first discovered when Kettle Creek was said to hold Brooks up to 18" in length. While that fishery is still great and I've caught 12" individuals from it, I theorize that Browns are part of the reason that fish of that tremendous size are no longer present. Do I love catching Browns, of course! Who doesn't? But I do feel that their presence is unnatural
Realistically, many of the streams that once held brook trout are no longer healthy enough to support them and if there is an open predatory niche that needs to be filled, brown trout may be the perfect solution in some cases (that is, until they get 30" and start trying to eat ducks LOL). However, I do believe that the streams that can and do still support native brooks should be protected as much as possible and Browns should not be stocked or present at all in these creeks.
While this is definitely a stream fishing oriented forum, I've had another similar discussion on some Great Lakes forums about the Lake Trout vs. Pacific Salmonids problem. This can locally be applied to Lake Erie where native Lake Trout are currently not able to reproduce due to poor water conditions and egg predation by gobies. Due to this, they must be stocked annually to ensure the population goes on. And while only 160,000 lake trout are being stocked yearly in the entire lake, a massive 1,000,000 steelhead are being stocked every year in PA alone. This is even more annoying as Steelhead show very little natural reproduction and the only reason they're being continually stocked is because Lake Trout don't run up the creeks to spawn in the fall where the majority of anglers can target them as Pacific Oncorhynchus sps do. But anyway, I'll stop rambling about Lake Trout (for now).