I think I've got a Paragon to do the same thing.
Paragon vs. Paragon mission
mod.
If the other Paragon gets the sensor array, the player Paragon on autopilot will not engage it. It will just wander randomly around the map, occasionally taking tachyon potshots if it sees the other Paragon. Without an engage command, anyway, which, ironically, it seems to usually win.
In related news if I refit it to have harpoons it will almost never use the harpoons.
I'll keep testing to see if I can coax it into acting sensibly.
Edit: the tachyon lances alone, without the sensor array, seem to be enough to make 'search and destroy' useless. It just runs away from the other Paragon until it can't see it, then wanders randomly.
Grabbing the sensor array myself makes the other Paragon run away and refuse to engage, making it almost completely incapable of harming me.