Since this movie series is arguably the most reality-based Batman to date, maybe Nolan could choose to simply keep the Joker in Arkham forever. No escapes or revolving doors. Frankly the Arkham escape rate in other media is the equivalent of Highlander's 'where do they hide the sword?', in terms of having to ignore a regular plot device. The guards and staff in Nolan's Arkham aren't soft-hearted fools, and we don't see them, alive or dead, because they know how to handle supreme psychos, having taken their lumps in the Crane breakout. They don't approach them when they're ill without serious backup. They are vetted for being in cults or like that.
Just so this doesn't gut the Joker's concept, you could establish that he is under a separate security system so that even the 'mass Arkham breakout' trope doesn't get him out. More, you could have in BB3 Gordon disgustedly reading this quote from the Joker : "Why ever would I break out? I went to a lot of trouble to start this show, and now I wanna watch it play out."
Maybe this was meant to be merely Joker's first strike. Now, it will have to be that TDK was his 'masterpiece' and he is content to sit back and enjoy the chaos.