Gentlemen...there IS a way to defeat this level, just read on...
For those interested, I found a MUCH quicker and better way of beating this mission. Go ahead and blow away the gunboats, the mines, and the minelayer (why not, extra points!). As Aeron heads out to the communications satellite, head towards that colorful nebula which is where the ETR with Zero-G units will come in. Be sure to have the lasers on full charge, and ignore the shield settings (but do make sure you have plenty to spare). As soon as the ETR hypers in, IMMEDIATELY destroy it. This way, there will be only a small handful of zero-g units which will mostly be going after you and not Aeron. I found this to be extremely helpful after losing some hair due to frustration.
There might have been some technical issues with this mission, but I had no real problems. In fact, I've defeated the entire game with no patch (even the official LucasArts patch which, for some unknown reason, bugs the heck out of the game).