Yes, you can create an AutoRestore exclude rule for the Genesis theme folder if you want. It would be better to create the AutoRestore folder exclude rule for just the Genesis theme folder then to create an AutoRestore folder exclude rule for the entire /themes folder since the issue/problem is isolated to the Genesis Theme. See the video tutorial link below for how to create AutoRestore folder exclude rules.
http://forum.ait-pro.com/video-tutorials/#autorestore-quarantine