Something to consider is that, in this reboot, Batman apparently dealt with and largely "fixed" Gotham some years back, until more recent days when things are going crazy again. This means that either Mr Freeze is a new villain ( not inappropriate, if he's part of a new wave of more over-the-top villains for a geared up JLA Batman ), or else they would need to decide upon his fate years back.
Personally, I'm partial to "Batman successfully reached him and convinced Victor to put aside his quest for vengeance", with Victor having spent the years since quietly working in some specially designed Wayne Industries lab working on medical research. I admit this would not make for a particularly useful movie villain.