Ouch...
First off, anything is way better than FM transmission, and with FM radio stations popping up everywhere, it's a good idea to have a plug.
Secondly, don't have Best Buy's Geek Squad do anything to your car audio! I had them look at a device for me, and I knew more about than they did. Besides, there are strictly car audio centers that do a better job at a better price. And if you look at Geek Squad's agreement, I believe they mention that they are not responsible for screwing anything up more.
In my Jeep Cherokee Classic, I have a custom stereo with an AUX input. It works great, plus if I'm on a road trip with friends or family, we can switch iPods out real quick.
Also, the 3.5mm jack has the same current/voltage output compared to the LR cable. It's just there's no cross frequencies between the LR like there is in the 3.5mm straight.