The beauty of the taxing system though is that if you don't want it, you don't have to have it. To disable it go to the in-game options, choose 'Gameplay' then go down to the bottom where it says 'AL Settings' and in there is something like "Sector Takeover Tax", set that to 'No' hit ENTER and the tax system will not affect your game.
Anyway the GOD engine SHOULD repopulate your sectors with stations (maybe it doesn't but it should, and if GOD won't do it, I will), and hopefully soon you will be able to capture stations, therefore meaning that the tax system could turn out to be quite profitable - if you play the system tactically.
I don't see you putting all your stations in your own sectors as ruining the economy, think of it more like wiping out some competition, then replacing that competition with your stations and reaping all the profits.
On a personal level I agree with you, I don't want my stations taxed, but I do want to tax the AI for my benefit, but thats because I like an easy game, some people don't like an easy game, and in the end I see it as more fair to tax both, so I relented.
Don't worry Russbo, I swear I will be doing something to ensure player owned sectors aren't barren soon. Just the claiming problem to fix first, and the respawning of enemy shipyards in player controlled sectors, and the......

---EDIT---
In fact I've had some thoughts about how I could 'artificially' populate player sectors with factories, shouldn't take too long either.... maybe I'll have a look at that soon.