Yes, there's no problem with atomic exchanges between multisignature addresses.
However you probably won't be able to use preparelockunspentfrom because that requires all private keys to sign the transaction on behalf of the multisignature to be in this node's wallet.
In this case, instead of:
preparelockunspentfrom <address> '{"<asset>":<qty>}'
you would use:
createrawsendfrom <address> '{"<address>":{"<asset>":<qty>}}' '[]' lock,sign
Then pass that partially signed raw transaction to other nodes for signing as appropriate before transmitting it with sendrawtransaction once all signatures required are there.