... which I only just thought of as I hit submit, is that the Doctor's presence on the TARDIS, within the Dalek ship, was required to keep the shields down so that the space-plane could attack. He planned to slip away as the ship fell apart, and since he left early to stop the bomb, the shields would have gone back up and the attack would have been useless.

So, maybe that's it?

They could have made it a little clearer, if that's the explanation. I find myself unsatisfied with the writing of this particular episode.