So looting civilian ships for engines and captives is the main way to make money?
You're a gang of pirates!
Hitting the big factions is a calculated risk until you start to become a major player yourself (and even then, one of the most important skills in XP is picking your battles).
You might also want to experiment more with fire, explosives, artillery and/or spotter/sniper tactics if reaction shots are messing you up. Also, melee. You might be surprised how effective a nude berserker can be if you learn to use her right. Some of my best fighters have never bothered with even the lightest armour - the incredible stamina regen rate means that once they've got a few fights under their belt, they can sprint more or less non-stop and still have the energy to cave a sucker's head in.
Spartans are a bit tricky to panic because they seem to have high discipline, and come with a lot of backup. But they go down fairly easily and aren't particularly skilled. I'm not really sure what to suggest, as while they often put up a respectable fight, they shouldn't be causing such a headache. Perhaps try using grenades or archers or artillery (the assault cannon is a deceptively effective weapon, especially once you've got a few alternative ammo types) to soften them up, as these don't tend to trigger reaction fire.
Hit and run is the order of the day, too, especially against humans. Don't assume you'll one shot them, but think of how you'll take them out of the fight - inducing panic, causing wounds and shock and generally wearing them down.
Also, never be afraid to kill a few people, grab their stuff, and leave. And if negative points are really a problem (not having a go here, but they shouldn't be that big a deal, so there's probably something going on), do poke around with the graphs screen (and note that you can scroll down on parts of it) as there might be intense activity in an area that you're not picking up. A spy zeppelin can be a real boon here.