The answer in this case is to conduct some UTXO management / pre-planning to ensure that there are sufficient UTXOs belonging to this multisig to allow createrawsendfrom to be used with lock multiple times in parallel. For example you can use preparelockunspentfrom or more general raw transactions (use appendrawtransaction to build up multiple outputs going to the same address).
As to the broader question, UTXOs are indeed used throughout MultiChain, but moving away from that would not make much difference. Instead you would have transaction sequence numbers and a later number would not be accepted before the first. Blockchains needs one method or the other to prevent replay attacks.
Another alternative is use Smart Filters in MultiChain 2.0 (alphas) to build your own multisignature logic, where each stage of the signature can take place on-chain. Essentially replace a 2-of-2 multisig with a 1-of-2 multisig and use inline metadata to represent and propagate the signing states and intended destinations.