One immediate solution is to use BitVise Tunnelier
http://www.bitvise.com/ftp-bridge provides a SFTP to FTP bridge, Tunnelier can normally be used free of charge if it is used by less than 5 people and on less than 5 machines in an organizational department.
We plan to offer SFTP support in the future, we're just not entirely sure how it's going to be done, at the moment simply dropping SFTP into the existing FlashFXP code base isn't an option. One option would be to rely on something similar to the Tunnelier but have it completely seamless.