Bathroom Fan Dilemma

Hey folks, 
We are remodeling the bathrooms (with permits) in our Marin County Eichler and have a dilemma. According to city code, we have to install fans in our bathrooms. However, our contractor is having trouble figuring out where to put them. We have 3 options: 
1. Put the fan in the ceiling by drilling the exhaust through the celing and vent it through the roof. This is the option our contractor prefers, but we don't want to do it as we just had a foam roof installed 4 years ago and don't want to put holes in it. We contacted our roofer and they said it would cost $2,500 to send a foam crew out to refoam around the holes so we don't void the roof warranty.
2. Put the fan in the existing hole for the skylight. We would lose the natural light from the skylight but there is already a hole there. Our contractor doesn't seem to want to do this option due to the electrical wiring that would be required.
3. Put the fan on the wall inside the shower enclosure, about 7 feet up the  wall opposite the shower head. This is our preferred option as it would enable us to keep the skylight and let the fan vent out the exterior wall, but the contractor doesn't like it because he feels the fan might get wet being inside the shower and it won't be high enough to draw moisture out.
Any ideas? If you installed a fan inside your shower room, where did you put it?
Thanks!