Farming rebel controlled sectors?

Solution 1:

The rebel ships you encounter after the sector has been taken over are intentionally harder than you would experience normally. They've got heavier shields and better weapons than other encounters in your current (or even usually your next) sector.

The rewards are also minimal at best. Just enough to keep you running.

You are unlikely to profit from these encounters over the long run. In fact, hanging around and fighting the pursuing rebels is usually a quick way to get a game over.

Solution 2:

If a goal of your play-through is to get the highest possible score for "beacons visited," then it might make sense to visit some extra beacons where the rebel fleet is present before leaving a sector, if you're confident that your ship can stand up to the extra punishment.

Solution 3:

No it doesn't make sense to not run from them. The rewards are just 1 fuel as to be able to move to the next beacon.