Jumping is the real problem with them and should be the priority fix. Once that's fixed just make it really slow. It's already completely vulnerable to piracy. I'd really like to see tradelanes refuse them due to size ("unable to accomodate ships of your size"), and remove the cruise engine. Then give them speed that is a little slower than the time-for-credit ratio of four 5k ships. I'd like to see 6 implemented somehow but that's too punitive with the massive drifting and no cruise engine.
I'd also like to see house 10k ships with the same limits.