Yes, it isn't a perfect solution. I guess though it depends on whether you just want a system to play right now or if we are talking about a future edition of Spacemaster. If the latter, you can develop entirely new attack tables that might give some room to maneuver.
Another option I thought was to say that higher tech weapons ignore or reduce some types of lower tech armor. You could say for example that ballistic weapons ignore any light or medium armor, treating the opponent as AT 1. A leather jacket doesn't stop a bullet.
Or, you could make a more specific system by saying that high tech weapons ignore a certain # of armor levels. So, using a Ballistic weapon on archaic scale armor (AT 7) reduces the armor to the effectiveness of AT 5. Different weapons could be given different reduction values.