There's not really a notion of pausing asset transfers in a blockchain – once a transaction is broadcast by a node, it is processed by the entire network. MultiChain's pause and resume APIs will not help with this.
Could you think about your needs in a different way, e.g. using a multisignature address to lock assets under two signatures, or having some kind of approval granted by a particular address in order to allow another address to transact, enforced by a smart filter. If you want to provide more information we might have a concrete idea.