Flint currently supports posting messages via AppleScript, which you can do like this:
tell application "Flint"
post "<message>" to room "<room name>"
end tell
This command can also be run from the command-line like this:
osascript -e 'tell app "Flint" to post "message" to room "room"'
If you want more commands supported through AppleScript, let me know - http://giantcomet.com/support