I am wondering if there is any way to survive the ion cannon from one of the imperial ships and then kill them?

Nope, not that I have ever heard of.

They are part of the game... no you can't kill them but you can trap them...as long as no one attack someone in fedspace..

Being the kind who wants to try things myself instead of taking the word of others, I made a ship with 400,000 fighters, 16,000 shields, and 8.0-1 offensive and defensive odds. those are the maximums the game allows. Then I tried attacking Zyrain, Nelson, and Clausewitz five times each. You don't even get to attack them with a fighter, and your ship ends up podding every time. It's automatic.

You can trap any of the three ships by simply putting a fighter in each sector adjacent. Nelson and Clausewitz will stay trapped until a player or alien/Ferrengi destroys the fighters in an adjacent sector and frees them. Zyrain, unfortunately, will twarp to Fedspace anytime that somebody breaks a Fedspace rule (laying a fighter, attacking a protected player, etc.).

Thanks for the info