On the higher difficulties, unless you get lucky or are just really focused with your research options, you likely won't have proper weaponry to deal with mercs by the time you first encounter them. Your best option will prob be to run away, taking some small bits of their equipment with you if you can.
Arena assault cannons work well, due to the massive cutting damage. Another options is having a group of highly trained bugeyes spam terror and then try to MC one of them, then running said merc into your ship and killing/knocking them down so you can kidnap him and take his stuff. Cars won't last long against their gauss weaponry, and tanks won't last forever either.