You need to get something like a table knife and run it around the window
seal from the outside. If there is rust in there it can't be very well stuck,
although there may be places where it is. A little oil or rubber lube on the
knife may help (but you will need to remove it with some solvent before
reinstallation). I cut a bunch of flat pieces of sheet metal about 1½" x 3"
and put them around the window on the inside, under the seal to kind of act
like shoehorns to help get the window out. I lie on my back in the back of
the wagon and push the window out with my feet while the helper catches it
and does whatever else is necessary.

While you may be able to save the seal, it's not guaranteed.

Be sure you get ALL the rust out and prime and paint and allow plenty of time
for the paint to dry before you put the window back in.
--
George Downs Bartlesville, Heart of the USA!