They never had a clear idea what to do with Jason Todd's return*. The initial planned seems to be a sort of sympathetic (anti?)-villain enemy , because he committed a truly impressive amount of murder, arson and property damage through explosions and tried to kill Tim a bunch*. Then they sort of wanted an anti-hero Punisher instead. But also wanted to keep him in Gotham and in contact with the other bats, but he'd already tried to kill Tim about 3 times at that stage and Bats couldn't really embrace a mass murderer, Morrison did try at a sort of redemption arc in Batman Inc but.... Then N52 happened and it got worse because they still couldn't decide on what Jason was , and because of the changes to Tim, one of his defining features hating Tim for replacing him was gone.
It was never presented as an arc where Batman decided to embrace killing and Batman was actually on acceptable terms with most of the Bat Fam post Infinite Crisis already (Jason being the prime exception because of the whole murdering thing and Steph to some extent, he didn't really reconcile with her to post Return of Bruce Wayne). Batman's Loner / Family cycle thing is pretty perpetual.
* Probably because his initial return was actually Clayface pretending to be Jason Todd which was retconned into really being Jason , then swapping with Clayface later on.
* Tim has some really bad luck from Identity Crisis through the Return of Bruce Wayne with both Jason and Damian trying to murder him for nothing he could logically be blames for and all his friends dieing and getting replaced as Robin by Damian who had tried to kill him (a dick move by Dick ).