Well, all the Jalousie windows I've seen in the past had removable glass. Usually a tab or spring strip holds the glass in place. You could remove the glass and not have to worry about the heat damaging the glass.
Removing the glass strips from the outside is easy enough that it's the way some folks broke into houses. They'd remove the strips, climb through the opening, then replace the strips when they leave.
There's also a product made by Prazi called a Putty Chaser. It's run by an electric drill and designed to remove putty when reglazing windows. Depending on your physical design, it might work for removing caulk. http://www.praziusa.com/puttychaser.html