Danny,
The only issue that I can foresee is that if you're camper is like mine it can be somewhat uneven under the cover. Be careful how tight you tie the boat down if this is the case! I'm assuming that you'll be loading a plastic sit-on-top type kayak, so not such an issue, but if you're talking about fibreglass (or even carbon / kevlar - I used to be competitive) there is a good chance to crack or break the hull (think firewood over the knee!).
I would suggest that maybe a couple of the foam pool noodles may be useful to form "raised" mounting points might be beneficial, some companies also sell inflatable roofracks which strap onto anything these could be worth a look too.
I wouldn't worry about the kayak rubbing through the cover, as that would take quite a lot of movement and in my experience the kayak will slide out from under the straps / rope well before the PVC is damaged.
Hope that helps,
Anthony