EXEing scripts from a .MIS File?

I know that .MIS files are the same as .cs script files, but I wanted to ask if it was wise to either execute script files from a .MIS file, or to add other content in the .MIS file, such as variables, mission triggers, functions, etc.?

The main reason I'm asking is because we need to run mission objectives that are specific to each map we play, so I'm looking for the most efficient way to do them. If I can add all the imformation in the .MIS file, that would be fine, or at the very least execute the relevant script file from there. I just wanted to make sure that there wasn't any reason why this could or shouldnt' be done :)

Thanks a lot!