Those directories are owned by the webserver so one way to remove them is by having a php script delete them. Possibly the simplest way (BUT MAKE SURE YOU GET THE DIRECTORY RIGHT!) is to run something like the following:
exec( "rm -fr wp-inst/wp-blogs/main/smartycache" );

Do the same for other directories, but beware, as with any delete function, if you get the directory wrong you could delete stuff you want to keep!
I should document it, or link to it, but if you add ?clear=1 to the end of your site url it’ll clear the cache.