Pssst.... use the phoenix. With Vagabonds and screamers.

i used that thing b4. its useless in missions with the ion cannons. i use the shroud, besides, same 4 hardpoints! so i never use the missiles, find them in-effective. if the phoenix can cloak, then i'd definitely use it, but it cant, so i can nvr shake off the ion cannon tracing, (its got a range all the way to the yamato, why don't it take out the yamato ??) a range of some 500 K (i've tried) besides, i beat it!

You can fly around to the top of the ion cannon and it can't hit you (a rather large design flaw).

That's similar to my way of nailing Dark Reign...I sit out of range until I get the go-ahead to kill the shields, then turbo in with my wolverine to hide behind some of the armor, where I can then safely pick off plates and chuck a hammer into the core. Then weave and turn desperately to throw a lock-on while running from the bang. Ion cannons are evil.

Reaper: $200,000,000.
Rockets: $100,000
The look on that pilot's face when you launch a full pod of screamers up his tailpipe: priceless