Don't have NPCs scale based on rank, have them scale based on security levels and location. Elite ranked pirates only found in Hazardous RES sites and Anarchy systems with a population of more than 100,000, this includes USS's. Elite ranked war NPCs in High Intensity CZs only. In contrast, high ranked police patrol high security systems, up to and including Elite. Missions spawn NPCs appropriate to their difficulty.
Scale back the difficulty of all NPCs except at the three highest ranks. Buff Elite NPCs a bit more. If they get modded weapons, only the top 3 ranks can have them, and only Elite NPCs get the really good stuff.
And there you go. Issue solved. Traders can trade, combat pilots can combat, explorers can explore, and the game is better all around.
Scale back the difficulty of all NPCs except at the three highest ranks. Buff Elite NPCs a bit more. If they get modded weapons, only the top 3 ranks can have them, and only Elite NPCs get the really good stuff.
And there you go. Issue solved. Traders can trade, combat pilots can combat, explorers can explore, and the game is better all around.