We don't know about this specific case. But as a general point, MultiChain's API is backwards compatible with that of Bitcoin Core, so you should be able to do what you want. Of course if you use the Counterparty protocol for asset issuance you won't gain the advantages of MultiChain's native assets.
Also yes, you may find that certain bitcoin wallets don't like connecting to a MultiChain blockchain, because of the genesis block contents, a protocol version number, etc... You would really need to do some debugging to find out the cause of this dislike and to work around it.