You cannot configure Defrag at all in OneCare Tune-up, unfortunately. You can, however, disable scanning of folders and even an entire drive using Exclusions in the Virus and Spyware setup that will be honored during tune-up.
I don't know I'd agree that Defrag would harm a flash drive specifically, but I certainly understand the desire to exclude drives from Defrag for any number of valid reasons - including yours.
-steve