Alpha 19 of MultiChain adds a bunch of extensions to createrawtransaction to make it easy to build asset issuance transactions independent of the MultiChain wallet. See this page for more information:
You can give issuance permissions to a particular address, but keep its private key outside any node's wallet (e.g. by deleting the node on which you created it). Use dumpprivkey to get it first. Then, build issuance transactions using createrawtransaction (according to the instructions on the page above) which spend one output belonging to that address, and create two new outputs - one with the asset in (sent to any address) and the other with change going back to the same address. You can use signrawtransaction with the extra parameter where you provide the private key (see Bitcoin Core docs) and then sendrawtransaction.
This way you can create a huge number of assets while bypassing the current limitations of the MultiChain wallet.