I would think that the best way to do an add in card would be to have a complete MiniMig with all ports passable through the PC's Bus (Be that PCI, ePCI, or whatever) This way you could use your 9-Pin joysticks, or have your PC route the equivalent commands through the bus so that the MiniMig thinks that they are real 9-pin joysticks. The same with keyboards and mice. Give the PC access to a frame buffer on the MiniMig Card, and PC software could route it to a window on the host PC. This would give you all the benefits of the suggested video card without the problems associated with trying to get hardware banging software to work on non-integrated MiniMig chips. It could also allow for a Virtual MiniMig bus that would make adding any PC peripheral just (just??? who am I kidding?) a matter of writing drivers.
Of course, I wouldn't even consider buying/building such a card until I had at least one or two stand alone MiniMigs in the house.