Regarding John Peel, if you get a hold of the 'Rarities, B-sides and the Beeb' bootleg, it has a documentary where Marr, Mike Pickering, Peel, (I think) David Jensen and maybe one or two others (John Walters? I can't remember, it's been a while since I listened to it) talk about The Smiths inbetween recordings from the BBC sessions. What Peel says is basically what's already been mentioned, he certainly doesn't say anything that could be construed as negative. The bootleg is also available under a few different names, one being 'My Favourite Motorway Services', a bootleg taking it's name from a story Peel tells about meeting Moz at...well, a motorway service.
As for the roots of Wilson's beef with Morrissey, that seems to be anyone's guess. However, whether it was intentional or not from Wilson's side, I do indeed think it was, if not exactly a blessing, at least just as well that The Smiths didn't sign with Factory. While I love a whole lot of the Factory bands (particularly from the period where they would potentially have signed with Factory), I don't see how they would have fit in with that label and it's sort of artsy/druggie/dance music vibe.