@Tim: Sorry, we cannot include such an option. In our experience, many storage providers simply have too many problems with folder rename operations so we choose the "safe" way and create a new folder where the encrypted/decrypted files are placed and remove the original folder at the end. (Actually files are handled similar with the difference that Boxcryptor renames it to the original name at the end because file renames are handled better by the providers.)
@Alex: It sounds like you experienced a Dropbox syncing issue. After the encryption finished, Dropbox syncs the new _encrypted folder. If the sync is still running while the folder is renamed Dropbox is having problems some times - especially when it's a large folder. (That's one of the reasons why we do not automatically rename it back to the original name.) This should not occur if Dropbox sync is paused before the encryption process (and resumed after the final rename) or if you wait with the folder rename until the sync has finished.