Here's the only problem with that. Remember the OWL Sector event with the nanobots and how the Vanguard were panicked because he nanomites had gotten into and overridden out armor? If it wasn't programmed to be beneficial, it's could have very easily destroyed/turned the Guardians against one another. And that's exactly what SIVA did the the eight Iron Lords.
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We could always get warlocks to reprogram the SIVA...
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warlocks are pretty much books and magic, thats why they're called "warlocks" not "techmarines"