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Here's my take on this: I think that the Ninth Doctor, as he was at the time of Parting of the Ways, wouldn't have done what Ten did in Waters of Mars because he was holding on to the concept that he shouldn't change history, even if he could. He'd just recently been through the Time War, and it was implied that he had made the decision not to go back and try to change things on principle, that maybe he could have done something but he wouldn't because 'everything has its time and everything dies'.
By the time of Waters of Mars, I think it's implied that the Doctor has started questioning this belief. He has the power to change time, why not do it, who would stop him? Why not make things better? What has doing the principled thing gotten him? Had it been Nine rather than Ten in this position, after what he goes through in between, he might have ended up in the same place.
And I agree, the fact that Ten was travelling alone during the specials was part of the reason he ended up in that frame of mind. His companions grounded him, without them he became detatched from how 'normal' people live their lives in the universe.
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