Nope! You think they're going to repeat the same mistake as they did with Mortal Kombat on Super Nintendo? They wouldn't do that.
Besides, even if they did, it'd be understandable. If MK VS. DC were to be gut-wrenching M-rated, Jack Thompson (as an example) would start blaming Superman for video game violence. Come on, man! DC's a family-friendly company, you think they're going to show Superman tearing heads off!? At least in the SNES version of MK, Scorpion could still burn people, so that's probably why they showed the Flash as a target for incineration!