I suppose you could use a handheld device to search for faction modules, and just turn all neutral AI hostile when one is used in the area. It might be better to wait until NPCs are improved so that they can be deployed throughout a ship or across a planet to stop an invader with a scanner. To further balance the features, data from the device could be somewhat cryptic, such as a readout of "warmer"/"colder" every 5 seconds rather than a pinpoint or even general location.
It seems to me the feature would be easier to balance as a handheld device. It would require being out of a ship and vulnerable to use, and thus it could be countered by NPC guards, anti-personnel turrets, etc. It would be awkward but possible to use a ship to assist in removing a faction block, but that involves firing on whatever you're trying to remove the block from. If it has turrets, there's a good chance it will return fire!
In the end, if whatever you're trying to de-faction is defended by AI, turrets, NPCs, etc. You will have to fight to tamper with it whether your objective is to capture or destroy the target. I think that's balanced enough.
Note included due to large amounts of borderline flame on this thread: If you disagree, tell me why and use politely worded, logically valid arguments.