I've got it! Because people tend to conflate good/evil and order/chaos, but actually they're two different measures, like two perpendicular axes (you can have ordered evil, for example). RTD tended to make everything about morality, but really, goodness was never the Doctor's problem: he is the good man, that's who he is, he always wants to do the right thing, he always has to help. Even his fall in WoM had to be because he just couldn't stand not to help. The real issue was that his sense of control had been thrown all out of wack and the order/chaos axis kept screwing him up. And the Doctor does conflate good and control quite a lot--Ten had to be in control to be right, there's that whole exchange between Eleven and Kovarian about whether good men need rules . . . The Doctor doesn't need so many rules because he's not a good man--he needs them because he's not actually in control. But the more he tries to clamp down on his control, the more destruction he ends up causing, until finally his forceful bending of the universe to his will spawned chaos (in Melody) to rear up and devour him (mirroring! but not dark mirroring . . .).

So really all this is about sorting out the Doctor's order/control axis, and doing that will require him to give up control on the beach . . .