Despite claims to the contrary, my hunch is that WB is going to tie the MOS and TDK trilogy together, and then have that as the launching pad for Justice League.
The TDK trilogy was an attempt to make Batman as relatable as possible - what would Batman be like in the real world? MOS is taking a similar approach with Superman. As Goyer himself mentioned, MOS explores the idea of alien first contact - how would the world react if an alien being like Superman came to Earth? It would be nothing short of a game changer for human history. With that kind of approach, it's not impossible to tie MOS to the TDK universe.
And they can certainly get back Christian Bale as Bruce Wayne (and include JGL as Robin/Nightwing if they want). I think the concept of a "Justice" League can be very relevant thematically to Bruce Wayne's journey, and here's why:
Bruce Wayne's goal was to be a symbol, an inspiration, and at the end of TDKR, he pretty much succeeded. However, the film also made another very important point: that laws, rules, and structures have become shackles. It's the very reason why Blake quits the force. TDKR argues the notion that you need a person or a group of people outside of the system to combat true injustice. Even the ending shot of Bruce in Italy in TDKR can be interpreted differently: you can either see it as his retirement, or as a brief vacation before he returns to work and clandestinely begins his new mission (and Blake is his first recruit).
With the arrival of Superman on Earth, coupled with rumors of other impending alien threats, Bruce can come back out of the shadows and take his idea of being a symbol a step further. In other words, Bruce can take all of Ra's al Ghul's wacky ideas about "justice", and use them for something much greater. Hence, the "Justice" League, which would be Bruce Wayne's version of the League of Shadows. Bruce can be the logistical and financial arm of the group, and if necessary, put on the mask again when it is needed (and since Lucius can prove fraud on the trades, they can explain how Wayne Enterprises gets back on its feet).
IMO, it can be easily done without ruining the legacy of the TDK trilogy.