You didn't mention what car you're referring to, which would provide helpful info, but I think I might have some insight. The 12v turn on lead to your antenna is constant; my car is this way, and I assume they're all the same (feel free to prove me wrong though). From the sounds of it you're not using any of your stock stereo setup, but if you are, you might have an amp in the rear with a 12v lead that you could easily tap into to potentially save effort. I never knew my car had a stock amp in the rear untill I installed my basslink.

I had quite the reverse of this problem with my car. I rarely use the radio, and I got sick of listening to the antenna go up and down when I turned the stereo on/off while listening to CDs so I wired a switch into the turn on lead to disconnect it, but to still be able to use it when I want to. My antenna no longer goes up at all, unless I tell it to.

My 420SEL had a really cool feature; there was a three position rocker switch on the dash that controlled the antenna. I could keep it all the way down, all the way up, or adjust it inch by inch to any position in between. Supposedly this was to avoid interference or distortion or something from having too long of an antenna (one of the longest telescoping antennas I've seen). I think it applied more in Europe though, for whatever reason.