I try to not rely on trade routes for income. At best, they are only a means to an end, as you eventually will lose ALL your trade routes. Instead, I focus on tax income and morale, and have no problem having idle planets. If your facing a large expence, shut down those constructor pumps for a number of turns.
I know for your current game it's like closing the barn door after the horses got out, but I try to plan my wars a little bit, in that I not only want to design and build/upgrade ships to match/counter theirs, but I also try and bankrupt them first, so that they can't counter-upgrade without totally killing their economy. Selling them a bunch of useless techs is a good way to do that.
Try using off-world population before hand also. Before I attack, my transports are already in space and full, with the planets full as well. The loss of tax income trying to fill up transports during wartime can be a killer....or so I have heard
Stringing trade SBs along the entire trade route is an expensive endeavor. Watch you route income per ship. I will set up several trade bases near my economy planet and reaching out 2-3 sectors. Once the trade ship is no longer in range of those SBs, destroy it and re-create the route. This maximizes your trade income, and keeps those trade ships in your sphere of influence and protection.