I'd like to know what world that people live in to think that traders are in any way defenseless, or should be so, against pirates. It certainly can't be this one.
People try to protect their investments from those who would take it. Traders have very little recourse than to pay or die currently, which doesn't make too much sense if you think about it for more than a few seconds.
There's an easy, but time consuming, way to change this without introducing any kind of death mechanic, but pirates dont want to be forced to organise against a lone trader (even though, as the attacker, that's exactly what they should do; defenders should choose their response).
That would be to make the commonly traded commodities cost a lot more to buy (and probably make bases consume less of them in return for the increased cost), so it actually becomes cheaper to pay the pirate in absolute terms, rather than in waffley opportunity-cost terms. Then of course, pirate demands go up as well, but there's scope to make some cash without relying on the trader's emotional, rather than economic, status.
Then you just strengthen the guns of traders, so they dont fall off after two novas, and do a bit more than scratch a shield.