I think that Rasputin was restraining SIVA, and activated the rest of his defenses to use them against the Iron Lords to prevent them from getting to SIVA, as he knew SIVA was an out of control prototype that would destroy everything, but when the remaining Iron Lords broke through, he released the restraints he placed on SIVA as a last resort.
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Rasputin wasn't restraining Siva. Siva requires a mind to control it, that's why it's been dormant since the fall of the Iron Lords. Siva was not a prototype it was a finished product. Rasputin even sent Siva into deep space to colonise other worlds under the control of the ship's sub-mind AI. Rasputin is not the hero or ally people think he is, he cares nothing for humanity. Rasputin bares a lot of the blame for the collapse.
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Rasputin is neutral. SIVA does need a mind to program it. But once it is programmed, it will carry it out until it gets reprogrammed.