I'm assuming this is essentially just there to ID the car as belonging to a contractor in order to allow the client to manage parking?
If so, would it be feasible to display the magnet inside the car? on the dashboard or similar? That way it's still visible but you don't have to worry about attaching it to the paintwork.
If this isn't an option there are steps you can take to protect your car's paintwork (I'm with you on this one.. I can get very picky about protecting my paintwork!).
- Make sure the paintwork has a good coat of wax or sealant on it.
- Keep a bottle of Quik Detailer (similar products from other manufacturers are available) and a supply of clean microfibre cloths in the car
- When you need to apply the magnet a quick spray of the Quick Detailer and buff it off with a clean microfibre and then apply the magnet.
- Sunbaking is unlikely to be an issue (only certain types of paint are affected - Vauxhall's red paint in the 90s and the SEAT OVNI Yellow are the usual suspects) as modern paints are much better at resisting it and the relatively small amount of time it will spend with the magnet on relative to the car's life will mean any difference is negligible. You can always vary the location you apply it too though if you're worried or know that your car is susceptible.
If you'd like some more information on options for protecting your paintwork see here for a primer (no pun intended).