Alot will depend on what type of paint is over what.
IIRC, the Joust cabs had stencil-painted graphics on the side.
If you are fortunate enough that someone painted over these with latex, you should be in pretty good shape.
There are several different types of stripper that will remove latex without attacking enamel paint.
If someone used enamel, you are in pretty rough shape as far as saving the side art.
One thing I have seen done by others is that they traced the sideart after partially uncovering it.
If you can get down to the point that you can SEE the sideart, but it's still covered in spots, you can trace it out, and then re-stencil the sides after stripping them and repainting.
As far as whether it's frowned upon to MAME the cabinet, that will vary by individual.
If it were my project cab, I would try to return as much glory to the original as possible.
If you can restore the side art, and get replacements for the marquee and monitor bezel, that's the route I would go for now.
I would keep an eye out for the other parts needed to return it to dedicated cab status, and do so when I could.
If the CP is still in a state that it could be restored to original, I would remove it and build a replacement for it.
The original CP on the Joust cabs is pretty small for a MAME cab anyway.
There is a good thread on here somewhere about a guy that built a Centipede cab with a Dynamo-style CP.
That would probably be a good route to go with a Joust cab as well.
The main reason that I opted to build from scratch is that I wanted to be able to do anything I wanted to, without any guilt about destroying an original.