Go ahead, as long as you don't plan to sell mac versions without donating back

As for missions and everything else, plans are always a bit shifting (LinWarrior is some kind of sandbox pet project).
You've noticed there are some small preparations, so you could subclass that mission base class to begin with.
Of course you could try to make a mission-file loader that:
- defines terrain (land is fractal)
- defines terrain modificators (modifications to the fractal land - ie. make plain land here and there)
- places objects
- sets objectives (fail if this or that object is destroyed, success if this or that object is destroyed - or totally different conditions)
- defines player party (a follows b)
- defines enemy parties
What's lacking at this moment is the ability to control the mech model and texture (these are randomized/hardcoded in the mech class).
Same with the Planetmap terrain type.
I think you could adapt that if you've come that far.
Make me proud
I myself (currently) plan to add a console / command-language which may ultimately may be used for missions.
But it may be a good idea for you to structurize your mission scripts like commandline commands, too.
If you'd like to make such mission-commands you're welcome to discuss possible/necessary commands here in the Feedback, Ideas & General forum.
[edit: changed forum for follow-up-discussion to Feedback, Ideas & General]