By this point, al Ghul is essentially dead in this universe and Talia has been putting the plan into action for 8 years. You could say it's because of revenge or a stubbornness that just won't go away over so many years of putting the plan into action - but the most likely answer is, that they are flat out evil and have set in stone beliefs about Gotham and what needs to be done to it, no matter how 'cleansed' it seems.
I guess evil organisations aren't big on second chances.
Funnily enough, a lot of the plot holes in this film could have been sorted out by just... not adding certain scenes. If we'd never learned about Bruce's leg or the fact he'd lost all of his money (which ultimately didn't seem to matter at all) two of the bigger plot holes (how'd he get out of the prison, how'd he get back to Gotham) could be explained a little easier. I mean with crime basically gone, the reason for him not being Batman any more could easily have been that he's just getting older and hasn't been keeping in shape, he's just spent the last 8 years moping over Rachel's death and not being able to move on from being Batman.
I don't see how him getting back to Gotham would be such a plot hole. He spent several years travelling around the world on his own with few resources. He's had the ability to get from one place to another while going under the radar for a while now and he had twenty days to do so. Also, I thought those were the reasons he hadn't been Batman. The leg thing just seemed to be on top of everything else that had happened as opposed to a reason for him hanging up the cowl.