In the Battle of Canary Wharf, all of the Daleks and Cybermen were sucked back into the Void, not necessarily killed.
Besides that, the Doctor may not have thought that genocide was necessary at the end of Journey's End, and was possibly disgusted by the fact that a "younger" version of himself would have done that. As he said at the end of that episode, the "younger" Doctor was himself at the end of the Time War: a much more ruthless individual. The Doctor has grown (or would like to think he has) through his travels with Rose.
EDIT: Additionally, at the end of the battle in Journey's End, the Daleks have very much lost. They're helpless, they've been disabled, and the planets were all returned to their proper positions. Genocide wasn't necessary at this point. In the Battle of Canary Wharf, humanity was quite clearly losing until the Daleks and Cybermen were sucked back into the void, making it more justified.