Even without pillaging, you can still deny them the resources - you just have to park a unit over that spot to do so. My change takes some things away, but it took a lot of FUN away for me when every little fight meant that I'd have to micromanage the workers to rebuild everything.
I'm still looking at it, and do think I would most prefer to make it so that you can pillage mines (to deny access to obvious things) and camps (to deny access to horses and elephants, since those are used in early units), as well as railroads, but leave everything else well enough alone. I want to defend stuff that matters, not inconsequential little things that just add to the management overhead and take time away from something more interesting.
I could set it so that only Workers could pillage, but the AI is not programmed to make use of them in this fashion, so that would be unfair.
I could make it so that when an improvement I don't want pillaged, is pillaged, it is replaced by an improvement of the exact same type. So everyone could pillage normally, but it would only affect the improvement I want. The AI could not handle this change either, though, and thus would waste its time pillaging standard farms and roads that are going nowhere, and as such this easy solution is no good either.
Hmh. I do play normal games with pillaging active as well, so perhaps I will gravitate to just living with it (since the AI is geared for using it) and having a Stack of Doom hovering near my cities, to make sure I can kill enemies before they force me to build the same farms over and over and over again.
Ah, solution three: look at AI files, in case there is an improvement priority number there for each different thing. Then I could drop stuff like farms and normal roads somewhere where they'll never get touched. Should have realized that sooner.