I agree that this was ultimately an utterly pointless story, since nothing remotely unexpected came out of it, aside from (shudder) "Jason's got a sec-ret! Jason's got a sec-ret!"
I can easily imagine that Tony Daniel has expressed an interest in doing some writing to DC editorial in the past (as artists do, look at Perez and Davis to name but two), IIRC Morrison tends to interact a lot with his artists when he's writing, so Daniel would have been more in the loop than most. It's entirely possible (though not known of course) that he astounded Morrison, DiDio and others in charge of DC with his love and awareness of the characters when he was involved in RIP.
So this was viewed as being suitable story for that, since the beginning and end were already known and the writer had been involved in the story that led into this. A gamble, but one I can speculate a logical reason for, not necessarily a wise one, but a logical one.
To be honest, and a fan of most of his work though I am, I would have had reservations about Morrison writing BftC, the way I have about him writing Dick in anything, since he showed NO feel for the character whatsoever throughout RIP. Dick was a cipher the whole time. I'm hoping this will change for "Batman and Robin"