While I haven't tried it, maybe you can combine freighters into a fleet with an attack ship.

Considering the relatively low cost of freighters and the difficulty in providing them with effective protection, I just keep some extra freighters to replace any destroyed. If you are dealing with pirates, no escort is likely to be effective and in war time I have had some success fending off freighter attacks without actually escorting them all the way. The AI seems to prefer blockade to search and destroy of freighters.

The logistics cost of guarding a trade route would likely make the route cost a lot more than it produced.

You're probably better off having some freighters on hand as backups, and/or establishing less potentially risky routes, and/or spreading out your routes so an enemy can't completely disrupt all of your trade easily.

In GalCiv1, if an AI was harassing your freighters, it would usually be with a small number of ships, so you could counter with a slightly bigger ship or group of shipsto patrol or clean up the area. However, your ships and fleets are valuable and sending them all over on wild goose chases is rarely worth the "opportunity cost" either. Overreacting to an attack on a trade route could open you up to an attack on a much more valuable planet or something.

I'm not sure that GC2 does the same thing, but in GC1, the longer a trade route had been running the more money it brought in, and I'm not talking just the higher bonus the further along the path. In this case, replacing an established trade route with a new one is still somewhat of a loss.

That said, Galactic Privateer is your friend.

it should be noted, however, that the Dread Lords ignore the Galactic Privateer, so I don't know if it works on "Minor" races.

I always like a GFE experience. The best site I have found is www.darwinescortservice.com. They are little pricey but have had some of the best time of my life with these girls. I guess you get what you pay for. What is the most you have paid for escort/ hooker?