That depends on if they would allow them to make the game true to the MK roots. The thing with MK vs. DC is that DC does not allow a M rated game that involve DC characters. In effect this makes the whole draw and appeal of MK games vanish.
People don't play MK games for the fighting mechanics, they play them for the over the top violence.
With MK vs Capcom (or SF) I'm pretty sure it'd be handled the same way. Capcom's other fray into the "vs" category in the past can be used as an example to this.
But, a MK vs. SF game would be a different game all together, especially if Capcom was the developer and not Midway. They could revitalize the MK brand if I would say so myself.