The internal wallet of multichaind is fairly straightforwards, and does not support HD. However you can use any external wallet or library to create HD keys/addresses. Anything compatible with bitcoin will work fine with MultiChain.
You might want to make life easier by setting up your blockchain for bitcoin-compatible address and private key versions – see the top of this: http://www.multichain.com/developers/address-key-format/
Also note that the permissioning in a MultiChain blockchain is per-address, so you'd need to decide how to handle that if you want to use many different HD-generated addresses.
