Well, you won't have any problem "playing" the game, in the technical sense that you will be able to connect the PCB to the JAMMA harness, insert a quarter, press start and fight the computer or another person.
However, you will only have access to the punch buttons. Capcom fighting games use a separate kick harness for the kick buttons, and the one from MK won't work.
Also, if you're using the original MK control panel, you will only have five buttons per player, so even with the Kick harness you will still be missing one button.
And you will have to use the MK button layout, which is just awful for Street Fighter.
BUT, making new control panels for a MK cabinet is very easy. You could replace the control panel on one of your cabinets with a SF style six button layout like I did with mine here.




Sorry about the quality. My camera is a decade old and I'm a terrible photographer.
I built my control panel out of a Door for a bathroom fixture I found at lowes. It was about 7 dollars or so I think. It was white, already smooth and finished, and the right thickness for controls. After a quick couple of passes on the table saw and an hour with the hole saw I had a new control panel.
If you wanted to do this, you could also just put your MK and MKII pcbs in the same cabinet and just switch the harness whenever you wanted to switch games, that way you are still able to play MK when you want to.
I'll add that MK cabs are great to play Street Fighter on, way better than the original Dynamo cabs that World Warrior came in and you mostly saw Champion Edition in and
almost as good as the dedicated Champion Edition cabinet.