Personally I would skip on the pitlocks/pinhead skewers. Why? Gator grips... Moving on;

I think it would be best to use a cable and u-lock combo. Cable strings through the front wheel and part of the frame, u-lock goes though the back wheel and seat post. The cable should go like a lasso around the front wheel and frame, and the other end should string through the u-lock. Using a mini is probably not going to work, get a u-lock that is at least the 'regular' size, or 'large' if you feel like you want to lock up to just about anything. A regular one should do though, and you don't want to get a u-lock too large because it can be pried. The seat has a quick release, I'd probably take that with in into class. One more thing to make the bike less desirable.

What to do about the weight? I would recommend a rear rack as the bike appears to have the eyelets, and probably really great considering you might be hauling stuff for school. You mentioned trails and different terrains, but I would say you would be able to switch to more slicker tires depending on what kind of trails you had in mind. If it were light trails that were flat, you can probably get away with slick tires. I think you'd need ones with some bite if you were going up and down slopes.

Continential Touring Plus or TravelContact look like they would be a good set to toss on the MTB but I'm sure other people would have better recommendations since I don't know MTB tires sadly.