Sure some guys can't do it right so you find a shop with some examples of their work still in the yard and look at them to see how good of a job they did.

I could be wrong, but I too thought the glass came out from the inside. If not, like you said it's a good excuse to have the top removed then fix the rust spots and redo the top.

I'm sure you already know this, but replacing that top will be a bit expensive. If the price is prohibitive then just remove the top and have it painted as another poster said but you didn't like, but maybe that's because you haven't priced the replacement top yet, combined with the glass and the rust. It's going to cost you more then the car is worth to do all of that. Also painting the top will get you better gas mileage.