Robbie,
The issue just now is the definition of "native". The powers that be seem to be extremely inconsistent in the application of the rules.
Mike can offer much better advice on the stocking of Rainbows, but it seems some areas you now need permission from the Scottish Parliament, others you can just stock, no questions asked (I dont believe this is the way its meant to be).
At the end of the day the only Trout in the UK that is native is the Brown Trout. All others are alien species.
There are many many fish that are truely native to mainland UK (Roach, Bream, Pike, Perch etc) yet they are not allowed to be stocked North of the border in new waters, but other fish, such as those from the aquatic trade, can be stocked in a garden pond (When does a pond become a loch?), right next to a river without permission.
The "green paper" was a great idea, but without an independent body to advise/enforce it seems a bit of a free for all in some areas.