A cheap way to deal with NPC Anacondas is hit-and-run. Fast ship, biweave shields, and at least some long-range fixed lasers or railguns. Go in, hit them hard to knock a chunk off their shields, then boost out again, staying out of range while tapping them now and then with your long-range weapons to mess up their shield recharge. Repeat until they're dead.
I've killed one with a Cobra III that way, though it was extremely boring. More fun in something a bit tougher where you can spend at least some of the time also using short-range high damage weapons like plasma or frags to take lots off its health at once.
(But yeah, you're not really supposed to fight the opposition on these missions ... they're just there to add a bit of urgency to what would otherwise be a very boring "find signal source, scoop cargo, go home" trip)