Actually it's not very logical from a business standpoint. PS3 needs a killer ap (they've really only had one, Resistance) and this could have been that game, it could have sold a bunch of systems.
It's a first party game so they should have had early access to a development kit and plenty of time to learn it. The argument of not wanting to learn new code/hardware sends a bad message to third party developers, if Sony in-house teams are intimadated by it, how are we gonna fare? While it's nice to give PS2 owners one final hoorah, it's not needed Sony has provided plenty of incredible games to PS2 owners over the years, but now it's time to look to the future.
They could have also taken the approach Nintendo did with Legend of Zelda and release the game on both systems with additional functionality for the PS3. Better yet, use the GRAW example from last year, Xbox and 360 both got the game, but the 360 version showed just how much better games can be on the 360. However, instead the development team was drinking the Sony Kool-Aid and felt that PS3 didn't need a great exclusive game, the pure power and ability to play Blu-Ray movies would be more than enough to sell the system. So PS2 owners can still wait a while before they feel a real need to upgrade to the next-gen.