Yep, let the pro's do it... Get a good one, because even a crappy "pro" installer can install a leaky windshield! I would get the frame painted, then rustproof the crap out of it. (a good formula to follow) Let the frame sit for a few days to a week or more to let the paint harden up good, and then have the glass installed. That way you can leave the frame and have them set the glass at the shop when they can fit it in.. I say give them a set time frame, maybe a few days to a week. Now you can install your new, rustproofed frame, on the Jeep and it will last a long time!
** Home brew "WaxOyl" rustproofing for cheap!
2.5 quarts of turpentine
12oz of beeswax (cheap source in the form of toilet bowl rings, pure beeswax)
1qt straight 30wt motor oil (non-detergent, made for small engines. You can buy at Tractor Supply)
Shave slivers into the turpentine until dissolved and then add in the motor oil. If you need to thin it out, you can add more Turpentine, or more wax to thicken. You can spray this with a garden sprayer just like any other rust proofing, just keep in mind, it will stay as a waxy film. The beauty of this is the wax and oil mix will soak into rust and the oil will stop it, while the infused wax retains the oil. The stuff also has a slight "self-healing" property where it will flow back to cover scrapes of not huge. For the windshield frame, I would take the freshly painted, (with nice hard paint after sitting a week) and seal the holes for the hinges top bars with the bolts or earplugs. Then install screws over for the visors and such. You want to close up as many holes as you can. Then, start to pour it into the frame from the wiper holes near the dash (with the frame off) and begin to flip and rotate the frame all over to get that wax coating all over the inside of the frame. Make sure you get it in there good! That will go a LONG was from ever having a rusting frame ever again!
A garden sprayer with a wand is great to spray it around other parts of the Jeep, like inside the frame and floor pan. The stuff really works great!