The only ways I know how to disable them are through repair and science. Are these the only way? I want to do a dumb character build but don't know if I would be able to disable the submarine in order to get to the oil rig.
You could conduct a thorough search for RP release(s) that included an extra option to get to the oil rig, via Vertibird (because it is not featured in the last RP version). But that'd be a real yawner.
In your stead, I'd launch the Fallout 2 Explorer editor and 'somehow', 'miraculously' conclude the quest , before safely journeying to the remote oil rig base, on the tanker. In vanilla you can have the fella — Matthew — watching the BOS bunker's entrance to resolve critical issues with the tanker, after you brought him the aircraft manufacturing plans he was interested in, if you're playing a low intelligence build. So, I take by that, that developers didn't intended to give you a hard time arriving at the open-ocean facility, if you're controlling a dumb Chosen One.