Yeah, if you've already gotten a public key set up (and an account on the target machine), then scp is much easier and completely secure. magic-wormhole is more aimed at situations where you don't yet have that pubkey copied over. Or where your receipient doesn't want to give you an entire account just to receive a single file.

In fact there's a mode (kinda experimental right now) to use magic-wormhole to transfer an ssh pubkey into the ~/.ssh/authorized_keys on a new account. Ideally your site admin should be able to give you access to a new machine with a wormhole code, instead of having you email them a pubkey.