Before you go wild giving Damocles new toys to play with, just remember that canonically he wasn't finished yet. He was hooked up to NORAD and SAC traffic nets in "listen-only" mode. The war occurred before testing was complete, so he hadn't yet been as fully plugged-in as his designers intended (it also explains why there were a bunch of civilians in the complex when he had his little..."episode"). So if you stick to that limitation there's no reason to worry about him going "Skynet" on you, and you have a good justification for keeping his arsenal small.
Things like this are one of the reasons I tend to stick with the "retro" EotW scenario: it allows me to spend more time on the "forward story" rather than trying to update backstory.
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