I found a command line sftp client called sftpc from BitVise which was packaged in the Tunnelier software package. It allows me to feed in the password and run a command script, once it's logged in.
So, I created sftpc's script to change directories and upload files, then called it with shell_exec(). After that, I used PHP's various file functions to move and clean up local files afterwards.
This way, I don't need to manually recompile PHP with SSH for Windows, nor worry about interacting with the program. It's a single simple command line, short and sweet. 😃