Yeah, it'd be one thing if they were full of crazy Angel temporal energy that prevented them from time-traveling ever again, therefore getting stuck in the past for the rest of their lives. But the idea that the Doctor can't ever SEE them again just doesn't make a whole lot of sense.
It's possible that the Doctor feels that if he DOES see them again, the temptation would be too great to try to rescue them. Which is why he doesn't want to take the chance.
It's simple, he just plants the tombstone and off they go!