One of the sticking points of it all, of course, is how it fits into the world of the New 52. Honestly, it doesn't--and that's reflective of a judgment call that DC Comics made going into the relaunch. It's a call that might be questioned--but it's not unique.
In the same way that Morrison was able to basically carrying on telling his pre-relaunch stories, provided he avoided Stephanie Brown and let them put "The New 52" on the covers, Geoff Johns was similarly not forced to alter his Green Lantern stories to suit the New 52. In both cases, the other writers on staff, some working with the same character, seem to have been asked to behave themselves and make everything fit, which made things seem a bit wonky and which will likely be resolved once the auteurs in question are gone over the summer.
Even at Marvel, the Marvel NOW! relaunch hasn't reset every title and character--critically-acclaimed series like Hawkeye, Daredevil and Captain Marvel may carry the Marvel NOW! logo and cross over with other titles, but they're still materially and creatively the same books they were before Avengers and X-Men got new #1 issues.
And Warner Bros., DC's corporate parent, did the same thing with director Christopher Nolan. In spite of the fact that Batman is a massive, billion-dollar franchise for the film studio, they allowed the filmmaker to tell his story as though the Dark Knight Trilogy were the only Batman movies that ever were or ever would be. The notion that Batman might actually die at the end of last summer's The Dark Knight Rises was not a crackpot theory; many critics felt it was the only sensible way Nolan could complete the character arc he had created for Bruce Wayne, and some even felt after the fact that the ending Nolan set up for the character didn't work for that reason.
Even though Warners knew they had a franchise to worry about and probably a new Batman movie to launch in the next five years, they had decided to allow Nolan to "tell his story" and worry about the fallout from that at a later date, with the idea that they were confident he would create some special, unique and enduring. They had opted not to worry about whether it "made sense" with Man of Steel or a prospective Justice League movie, presumably because they knew the character had the kind of flexibility that would allow for a seamless reinvention in just a few years.
After all, for decades the popular perception of Batman outside of the comics industry was colored primarily by Adam West. Then Tim Burton came along and the game changed. Bruce Timm and Paul Dini changed it again, and then Christopher Nolan. Batman is reinvented on the screen almost as often, and with almost as much diversity of tone and content, as on the printed page.
Morrison got the same treatment, allowed to finish out his Batman Incorporated/death of Robin/Leviathan story in spite of the fact that so much of what led up to it doesn't work or make sense in the New 52 and the fact that Damian's character biography throws the timeline of the Batman books into chaos. It was more important, DC reasoned, to get resolution on this fan-favorite story than to force someone like Morrison to conform.
Given the massive commercial success and critical acclaim that both of these takes on the Caped Crusader have received, what's arguably harder to understand is how it wasn't affected more of DC's titles (although it certainly seems as though Zack Snyder has been allowed to make his stamp on Man of Steel, so perhaps Warner is hoping to emulate the success). The recent spate of creator conflicts with editorial at DC seem to suggest that Morrison and Johns may be the only ones for a while who will be allowed to go against the grain in service of a larger story, which is arguably too bad; while Scott Snyder and Greg Capullo have had huge success under that regime, the forced crossovers with other titles have weakened the line as a whole, and it would arguably be nice for someone to be able to do something interesting with Tim Drake, Anarky or some other tangential Bat-character without worrying about whether their great idea for a story conflicted with something that supposedly happened but hasn't yet been printed during the five-year gap.