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In those missions, even if you're pitted against traders or system militia, you won't take a rep hit for destroying their vessels. The rest of the time, you'll be squaring off against hostile Korian Outsiders, the Murath, or that goofy fish cartel, whatever it's called, and they aren't factions that control stations.
This can be a bit of a grind, so the best way to proceed, IMO, is to start gearing yourself up and doing the story missions to get a jump drive. From there, you can use the cash strategies like mining Faces of Gozu or finding gear containers in junk fields from higher-level systems. Once you're geared up, go back to an easier system and take Pirate missions from the merc guild. Yes, your faction relations apply across all sectors, so you only have to do this once.
Once you get your faction ships or whatever you want form the Pirates, just play however you want. Technically, it's possible to just keep restoring rep with them by making up for any story missions with merc missions. I don't. It takes too long and I don't like pirates. But as you go further through the story you will get fewer story missions dealing with pirates, so you can get to a point where you're just friends with everyone.
The only caveat to this is that you will almost exclusively limited to free trading and merc missions to maintain good rep. Almost every other mission will have you losing rep with someone, again, unless it's against the Korians, the Murath, or the fish cartel.