As you know this is one of the most requested and attempted mod ideas. Everyone's favorite scifi mod from trek to B5 would benefit from some way to make ships that are restrictable from jumping. I just don't see a way to do it that I like.
Your sector damage idea is original, I will give you that much.
Not sure it's practical though. For one thing, wouldn't you have to do that manually? Or is there some way to modify the systemtype file to do that.
What if you just made them really slow in normal space. Only one sector per turn. You'd still have the problem with stacking though.
Although, even if ships could be blocked from warping that wouldn't meet your needs for system boats, cause they couldn't be ferried. What you need really is a class of drones that can be recovered and given orders like a ship.
Geoschmo