I can take out the advanced trains just fine with my LSF gunboat... did just that earlier today when defending zone 21 from a smuggler trying to get through the gate.
The real problem is how useless Cruise disruptors (barring train cd's) are against them. I used nearly 30 cruise disruptors to keep him out of cruise while I shot him down, most of them had no effect, and the only reason I was really able to stop him was because I got lucky with the CD's that did hit properly.
Train disruptors work great against them, but if you use a train CD in any area with allied or nuetral NPCs, you can be sure they'll go hostile before you can snap your fingers. Unfortunately I dont see much way around this - most lawfuls would rather use non-train cd's for this reason, and it makes smugglers in trains very difficult to stop sometimes.