No need to remove the window. Removing the window unneccessarily will just make life harder.

 

The window is pretty easy to remove and gives you easy access to all the door handle hardware and linkages with room to work in the door if you have large hands. I've never done a handle swap with the window in, next time I do one (and I'm sure it will be sooner, rather than later, since I own 2 FCs) I'll leave the window in place to see how it goes glass-in.