I would probably just ignore them at first, I mean... come on, what could one kid against my seasoned troops possibly do? However, if he proves to be too much of a nuisance, I'll probably send some of my Elites to take care of him whilst I continue with more urgent matters regarding my master plan. Assuming he got passed them, I'd have to deal with him myself, but at that point, we'd probably be very close to the fruition of said plan... so, out of ego and spite, I'd capture them and make them bear witness to the results they were trying so hard to prevent, under very tight security.
Only after the plan is complete will I kill them.