is there anyway to use the code consol, or something similar to run code in multiplayer on a server besides user_scripts?

You answered your own question. Use the code console. Input code directly in.

im not talking about a game hosted off of my PC, rather a real server that uses black bag ops.

We weren't supposed to inject any code into the game in the first place.

For a dedicated server, you can use a user_script, BlackBagOp's remote manager, or the direct swbf2 commands sent through network communication. I don't know what the format of those commands are, but I'd assume everything useful is already included in the remote manager. If you do find a way to inject code through net commands, you'll destroy MP.

The only thing I know how to send to the server from a client is which unit to boot. Everything else is server to client communication.