The gill lice issue originated in private hatcheries and was transmitted to wild populations by private citizens stocking those infected brook trout. Disease is only one part of the equation, though. The state has greatly reduced the number of brook trout they raise and/or stock, which I give them credit for. Right now, however, several private hatcheries all over the state are still raising brook trout for sale to private citizens, and without any way to track where those fish are going, they may end up in native brook trout streams.
The studies on introgression looked at PFBC-sourced stocked brook trout, which are likely far less fecund and poorly suited for survival in the wild. These private hatchery fish today are likely more fecund and better suited for survival in the wild. That's evidenced by the existence of obviously wild offspring of a certain private hatchery's brook trout traits showing up in year 1 aged fish in the wild.
How much damage could disease or highly fecund hatchery brook trout cause in a Class A brook trout stream or an entire system? What happens when some private hatchery-sourced brown trout end up in an unstocked allopatric Class A brook trout stream? There is a significant threat to wild populations that might be irreversible by allowing the unrestricted sale and distribution of private hatchery-sourced fish. Much like the gill lice issue, it may be too late before we discover what happened, with no way to at least document what fish are going where.
No hatchery or nonnative trout should be stocked over wild native brook trout populations. Period. Regardless of the source or the party responsible for doing it. We can't say, "well, unless PFBC stops doing it, then private citizens should continue doing it too." Compounding the problem isn't fixing the problem. This stocking authorization is/was an opportunity to prohibit, reduce, or at least document what private citizens are doing. There's no downside to it. It's a free program that creates a paper trail for where fish are being stocked. I don't see how any fan of wild native or wild nonnative trout for that matter would have a problem with the proposed regulations.