I think your best bet there is to have your colony ships take a hike away from the intruders rather than sit around, they're less of a target that way. Then you should be able to intercept the enemy ships before they hit your colony ships.
I usually have a few ships sitting around in a front-line system that are loaded with as many engines as they'll take, plus solar sail, and basically no extra supplies. They can't go far but you can pack some extra armour and stuff in the space that would have been devoted to supply. Once you get a quantum reactor this is pretty much redundant though, since you can send those same ships to escort your planet-pounders out to enemy territory.
EDIT: Uh, I forgot to read page 1. D'oh!
[ June 18, 2002, 13:37: Message edited by: Marvin Kosh ]