What do you mean by 'automatically'? Are you refering to making a custom command that will delete the .svn folder tree, or are you refering to some kind of shedule to run/login/delete/close all by itself?
As long as you have the correct permissions, and have 'show hidden files' checked in your settings, you can just click the .svn folder and hit 'delete' and FlashFXP will recurse through the .svn root and delete everything.
Personally i think messing with svn should be done properly through the terminal. (infact as a last resort if these are old stale svn trees you could write a one line terminal command to recurse and wipe .svn folders for you)
Edit :: I am not sure it is possible to use a custom command to recurse the server, find all .svn trees, and recursively delete each (given the current set of commands availible in the custom command creator). However you could actually use the 'find files on ftp server' feature to recurse and find all the .svn roots, then select all the results you want to delete and right-click>delete.
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