Isn't the stated reason for the movie SS to fight high powered super heroes that get out of line? Fighting the joker in the first movie would seem to go against that mission. I mean, fighting one of their own people who went AWOL wasn't much better but at least it was kinda in line with their purpose.
The mission statement is the first thing out of whack. They shouldn't be assembled to deal with superpeople if they're mostly not superpeople themselves. And if they were superpeople capable of that, you then have to answer how were they ever caught and imprisoned. The whole premise just doesn't work.
A guy like Joker at least makes sense on a logistical level if he's a crime boss who's just really hard to get to without heavy casualties. You can write something reasonable around that.