I can't speak to the science, but I have noticed in my personal experience that my hair can tolerate occasional silicone product use in styling products, but not in cleansers or conditioners, and I believe it's because I'm not able to get enough moisture into my hair when I use silicones in conditioners.

Modified CG since 11/5/11
CLEANSE: CJ Daily Fix, DevaCare No-Poo, CHS Treatment Shampoo
RO: SS Caitlin's Conditioner, CJ Beauticurls Strengthening
LI: SS Repairing Protein Treatment, CHS Silk Leave-In
STYLE: Re:Coil, Curl Keeper, Deva Ultra Defining Gel, Curls Rock Amplifier,Sweet Curls Elixirs Okra Gel and Hard Hold Gel, SS Curl Enhancing Jelly and Firm Hold Gel