You can't "inactivate" screens but there are a few options to keep them yet have them not appear in the course map. One way is to set up a resource folder in the course and put the screen in there. To do this add a new folder and select the check box that says "this module is a resource". Any screens that are placed in a resource folder can only be navigated to by jump-tos linking them to other screens. Your other option is to copy the screen to your library first, then delete it. This will remove it from the course but it will remain in your library if you want to use it again at a later date. To do this you simply check the box "share this screen in your library" and click save. Then you can delete the screen.
I hope this answers your question.
Maria