Given that it is really, really hard to get full employment on any colony of significant size, because growth is way faster than construction, I'm not sure it's a great idea to penalise players for it. Besides, the "manufacturing" sector is just the TN installations owned by the state - there is a load of civilian manufacturing that produces trade goods that isn't accounted for in the jobs record.
Actually, that would be interesting. A fourth employment sector, "Commodity manufacturing" or "Civilian manufacturing" or something. Starts at 0, increases with the size of the colony (in line with the increases in trade goods production). Then you could have that affect trade goods production. If there was lots of trade and available unemployed workers, the size of the commodities sector would increase and you'd get more trade goods. Great for colonies that are just built for economic reasons - no mining or manufacturing installations, so lots of free workers = more trade goods. On the other hand, if there was complete employment in the TN sector, say at a mining colony where every worker was needed for harvesting that delicious Duranium, the Commodities sector would atrophy somewhat, reducing trade goods (not to 0, say to 50% of normal trade goods production for a colony of that pop). Import requirements, obviously, would be unaffected in both cases. If you want to also get exports from that mining colony, though, you'll need to plop down a few extra colonists than are needed for the mines - they can kickstart the non-TN manufacturing sector.
The advantage to an approach like this, over a broad penalty for unemployment, is that it doesn't add another factor that the player must micromanage. If you don't care about maximising trade goods production, you can totally ignore this addition and you'll probably never notice. But if you choose to invest a little extra time micromanaging populations to ensure a healthy civilian manufacturing sector, you'll profit from it. It also gives something for those "I only made this colony because this was a nice world" populations to do, like Mars when you get a bad roll on the mineral tables.