True, Edward probably wouldn’t kill Mary, it would upset Catholic nobles like Norfolk. As for Mary Queen of Scots maybe have Francis II did early and Mary head back to Scotland but get shipwrecked England and forced to marry Edward?
Hmm, true an Anglo-French alliance could last for some time. I doubt it would last though, the whole issue of Calais could lead to war. Though the Spanish Netherlands are in a spot of bother here with the Anglo-French relations. The French Wars of Religion would also be interesting.
I doubt Edward would treat Mary like you mentioned in the last few lines of the post, I think they could be too close for Edward to do some of that.
Why would they be too close? As far as he's concerned she's a heretic, she might be his sister, but she's also a heretic.