The removal of pillows is not about pathogens. It is strictly money. I have tried in my original post to deal with both. By "renting" a blanket and pillow, the package can be distributed in a wrapped and sanitized form before the flight. This would eliminate the issue of "contaminated" pillows and blankets (and furthermore justify the $5 rental charge). By renting them for $5 each, you would eliminate (almost) anyone not wishing to use them for what they were originally intended and CO would collect money for a service they once provided for free. However, in my opinion it would make the flight more pleasant and at least not further tarnish the image of CO. Furthermore, it could provide elites with a small benefit, and return pillows and blankets to F which should be stocked with such "amenities".
Come on guys, UA gives their F passengers pillows and blankets. Lets do the same at CO.