I've found a trick to exclude sftp-config.json from the folder you want to map with remote server. I needed that because I didn't want my server credentials to be synced in clear text on SugarSync (or Dropbox) and there is no way to exclude a single file from syncing with SugarSync.
So here is how I'm doing:
1) Create a folder anywhere which won't be synced
2) Move sftp-config.json into that folder
3) Create a symbolic link to sftp-config.json in my working folder (tested on MacOsX)
SugarSync ignores symbolic links but it seems it's not a problem for Sublime SFTP so that's perfect
Now it would be great to modify Sublime SFTP so it can do it automatically ; maybe adding an option "sftp-config-folder" in SFTP.sublime-settings, anyone ?