In the revenge of the Snathie scenario, one thing that made it hard was that the destruction of the survey ship would cause the game to be lost.

I noticed that if I head for an anomaly with my survey ship under which a Prison Guardian ship is hiding, that I am able to fleet up with the Prison Guardian Ship.   From then on, I can no longer control my survey Ship, but it is no longer attacked by the Prison Guardian ships, and this removes a vulnerability the Snathie have in this campaign.

Later on in the game, I am able to attack this fleet of a Guardian Ship and my Survey ship and destroy it without consequence.  

I don't know if it was planned that way, but this small flaw enabled me to beat the campaign scenario twice already.