If you store the script files on the client, in any form where you can eventually read them on the client, you can't "protect" them. They will always be open to exploitation, even when hard-coded into the game's executable or "encrypted" (as they must be decrypted to run).
You can prevent casual exploration by packing the files in some non-obvious format, but that isn't security against hacking either.
To prevent players from exploiting by altering scripts (or any other data), you have avoid placing trust in the client. Store everything you can on the server, transmitting commands to the clients (for scripts; this is how scripts in Guild Wars 2 work, for example). What you can't do exclusively on the server, make sure to verify on the server at least.
If you are making a peer-to-peer game, this is harder. Typically you'll want to employ "gossip"-based verification, where every connected peer (or some subset at random thereof) verifies actions and the results are compared to ensure they agree. You usually need to tune the heuristics involved to get a good play experience.