Ok, first off filezilla is not a good ftp program due to security being weak.
Passwords are stored on the file system in clear text in an xml file!
But hey, what do you want for free!
A much better ftp program and used alot in the underground is FlashFXP. Supports a huge list command line parameters and much more secure by encrypting the sites database.
Loaded with features but not free. I would assume a plugin for this would be required.
Please give it a look.
I will add this product to our possible add-on list. André, my colleague is continuously adding more add-on to our list. You are right for Filezilla, but here is the nice thing with RDM, you don't have to put your password in Filezilla, just us RDM to store the password and call let the application call Filezilla.