Just a heads up for anyone else with this issue, I found this .exe over at XDA (not the same one as wmdunn linked to but works perfectly:
http://forum.xda-developers.com/showthread.php?t=471181. I changed the Dword in the registry to 1000 so it checks ever second. Works like a charm when I manually turn off bluetooth, now we'll just see how well it works in the car!
I think this should be a fine (although not perfect) solution as it doesn't drop our during calls when connected, just while it's paired. Unless someone calls in the few seconds it takes to re-pair after bluetooth goes back on this shouldn't be a big deal.
wmdunn, thanks so much for linking over to XDA to help me find this!