What's going on with Thor in Fraction's run is that the Asgardians are searching for a new home. But if JMS had stuck around, I'm sure he could've simply given them an arc or two rebuilding Asgard and then gone back to business as usual with his human/god interactions. It's the difference between rolling with the punches and taking his ball and going home. JMS chose the latter and, frankly, Gillen's improved on where he left the series, so I'm not too broken up about it.
JMS' run started to suffer because he started to hastily wrap up his run in three issues plus a Giant Size conclusion, instead of allowing it to continue naturally. I think that if JMS didn't have to do such a thing, his run would have been just as fantastic as Thor #1 - 12 and #600.
JMS does have some valid concerns, but like clones said, the only way he's ever going to have full creative control is if he goes independent and does creator-owned work. Playing in the major publishers' sandbox has always come with strings attached. DC may have found it profitable to lessen the strings lately, but to me that just means it's a slightly different paradigm, not that they're necessarily encouraging creative freedom more. Plenty of other writers get changes thrown at them and develop whole new ideas out of them. It's possible to be creative and adaptable at the same time; hell, it's necessary at the major publishers because, again, that's the nature of the beast. Work on major characters, deal with the need for those characters to have a presence beyond your series alone.
But you still shouldn't have other writers who aren't even writing the character just pop in and change things like what Millar and Bendis did. Frankly, I find the lesser the strings are pulled and allowing the book to simply stand on it's own instead of constantly tying in, the better it is. Books starring solo characters like Thor, Superman, Amazing Spider-Man, Captain America, Batman, Wonder Woman, etc. should be left to their own devices.
Meanwhile, team books like Titans, Avengers, and Justice League should have massive editorial influence to prevent inconsistencies. This is where DC and Marvel fail though because you have DC's editorial ruining Titans and the Justice League while Marvel's editorial allows Bendis to do whatever he wants so Spider-Man, Captain America, and Iron Man feel like completely different people than the ones who are starring in the Amazing Spider-Man, Captain America, and Invincible Iron Man.
Also, I seem to recall DC trying fervently to throw plenty of changes into Morrison's work. The only difference is that DC's editorial, I assume, is laxer than Marvel's because they backed off and let Morrison effectively ignore everything they published in Death of the New Gods, Countdown, and other stuff. So are they really fostering creative freedom or are they just not as willing to put their foot down and steer the universe as a whole for the sake of their creators' egos?
I think that's more along the lines of DC knowing that Countdown sucked and Death of the New Gods being completely contradictory to what was going on. They knew they dropped the ball with Countdown and they knew that fans hated it.
That is an instance where allowing Morrison to say "**** it!" was for the best.