I have a 1988 300E with some minor surface rust along the top trim of the windshield that I would like to touch up. It looks like the trim panel is seperate, but I would like to know how it is held in so that I can remove it.

Start with the trims that run from the front to the rear.
Stick your fingers under the side trim at the top of the windscreen, gently pull it up until it gets out of the upper side clamp, gently pull the trim out of the two lower clamps (beware and watch out: the trim will stuck under the front fender edge, so you can take the bottom part of the trim out yet).
Pull out the trim along the roof clamp by clamp and after the last (rear) clamp let go of the trim, you can take it off the car.

When you have removed one roof/windscreen trim, you can remove the upper windscreen trim by gently pulling it out of its steel clamps starting at the side that is freed from the roof/windscreen trim.

greetingz,

Some idiot must have glued the top trim in when they installed the windshield.
 

I can't get it to come off and I fear I will damage the moulding or maybe break the glass. Any suggestions?

The idiot you mentioned probably has mounted the trim when the window kit wasn't hardened out! The kit will stick the trim; you can try to get it loose by gently pushing up the trim at more as one point.
If they stuck that trim in a lot of kit, the trim may become a total loss while taking it out...

greetingz,