The problem was that they wanted to use JLA as a centerpiece for some of the big stories they were telling, like Final Crisis and Salvation Run and whatever else, but they went about it the wrong way and just used the book as a launchpad, when really, a writer as skillful as McDuffie can be could have worked those stories as arcs of JLA alongside the writer of those events and made it flow a lot better without damaging what he's aiming for with the characters.
Or maybe that's just my perspective on these event books we keep on getting told we must fork out on. Why not make them storylines of a particular title and promote the hell out of them? Final Crisis in particular could've been told across a set of the DC books, as could Secret Invasion. That way, you get people picking up a regular, continuing series, and if they like it, they might stick around to read it.
But regarding McDuffie, I'm kind of divided over how I feel about him getting the boot, but I still don't think he's entitled to spill company secrets and talk about his boss and his work the way he has, at least not in such a public fashion. If I, for instance, talked trash about my boss on the internet and dissed the company I work for and they found out, I'd be dismissed too.