I'm sure Ironman as an EMP cannon somewhere. He just has to use it on the Batmobile with Batman inside. Batman can't get out, so Ironman just uses his proton cannon to blow it up and so long Batman. Starks heart really isn't a problem now that he has nanobots coursing through his body. I think both Batman and Ironman would do whatever it takes to get the job done, Ironman fought Captain America who is his best friend.
an EMP will nullify any weapons advantage Ironman has against Batman. Ironman would be just a guy wearing a paperweight tin can suit. Plus Tony Starks has a heart problem. Batman will do whatever it takes to get the job done.