bitcoin-cli is just the way to interact with bitcoind... it passes the commands to the bitcoind daemon and then returns the responses to you.
The wallet would already need to be loaded by bitcoind (which is essentially the same as having it loaded via the Bitcoin Core GUI) for the walletpassphrase option to work. Same with using dumpwallet with bitcoin-cli... the wallet would already need to be loaded by bitcoind.
So I'm assuming it would get mauled again, rather than being in it's original raw form?