I've done many of these over the course of my playthrough and they were doable back when the game started and up to about the midway point.

However now that the game is using all mk5 and mk6 gear on most enemies, ten gunships can EASILY destroy a single frigate (the usual defence target).
I can take on half of a fleet in my merc destroyer, but while I'm doing that, the remaining 2 destroyers and 10 gunships easily take out the frigate.

Even when it's a cruiser that you are to defend, all this actually means is that there's that many more enemies.
As far as I can see, these missions are impossible in the end-game and it's REALLY frustrating to play them now.