I don't think it would make any sense to remove the mirror in an MF camera. Might make sense to have a secondary mirrorless model to complement it but for sure not replace it.
Rather than removing the mirror if I had it my way I would make the pentaprism a removable module to turn it into a waist level viewfinder (optical). Not sure how much that is possible though because of the AF, exposure meter and possibly other things that might need the prism to work. Unfortunately there's no way I can afford a 645D, let alone influnece its successor's design
As far as mirror induced vibration that can never be a problem that necessitates doing away with the mirror entirely - you can always lock it up or use live view in particular situations where it might matter. Here though as already mentioned one would wish for there to be a more permanent lock up mechanism, preferably a direct mechanically linked lever as I believe the film 645 and even many 35mm film SLRs had.