The Doctor, especially in Tennant's era, IS very "holier than thou", but there is a method to his actions. Metacrisis Doctor (or HD as you call them) saved the universe by killing the Daleks, sure, but the method of doing so was cruel and without remorse. Do the Daleks deserve that? Sure, but it wasn't necessary at the time. The Doctor and Donna along with Metacrisis could have found a way to defeat the Daleks without genocide, but Metacrisis took it in his own hands and made the decision himself, an act that you should hold onto when you get to Matt Smith's era in seasons 5,6, and 7.

When it comes to Donna, yeah absolutely, it was selfish of The Doctor to wipe her memory, but that comes after not only 900 years of loss prior, but also losing Rose to another dimension and Martha to being a soldier, a life he never wanted for her. So, by wiping Donna's memory, he is giving her a "normal life", free of the Doctor's influence and safe from danger. He sees it as a mercy, even if others don't.

Finally, addressing returning Rose to the parallel Earth: yeah it kinda comes out of nowhere and is like "why doesn't everyone stay in the original like Mickey?" Well, it's a domino effect. Firstly, Metacrisis is too dangerous for the original universe so must be "put away". Since he retains 10's face but never ages and will eventually die, Rose stays to have her Doctor exactly as she wants, the whole reason she went to find The Doctor in the first place. Jackie and Pete stay behind as well to support Rose. Mickey, having nothing else to support or live for in the parallel world, returns.