If you are that concerned about your car, be careful with this option. I know it sounds counter-intuitive, but these can cause far more damage then drilling a hole. Magnetic dust and grit often gets under the magnets and creates rust swirls in your paint. Rain water gets underneath and sits there even longer than if there was nothing there, which does not help the rust problem any.
It really isn't hard or expensive to get a hole filled if you need to, or you can get a small antenna that fits in the same hole as well.
If you really insist on using a magnet mount antenna for a permanent install, consider putting a thin layer of silicone sealant between the magnet and the roof, this will help keep the magnetic dust and grit away from the magnet, and after removing the magnet rubbing your fingers over the sealant will pull it up. The sealant may also hold the antenna in place a little better as well. I would, however, call this a stopgap measure at best, but it is better than slapping a magnet mount antenna on your car and letting it do its damage. The problem with the sealant is if the antenna is knocked off you have to get all the sealant off before putting it back on again, and the sealant makes the capacitive connection between the magnet and the metal that is your vehicle worse, and this is a required electrical connection that the antenna has to have to function. So essentially, with a magnet mount, you are either shooting yourself in the foot, or shooting yourself in the other foot, the choice is yours.
Optionally, you can see if you can find a spot for a lip mount, they can be somewhat permanent and suffer none of the disadvantages of a magnet mount, although you are more limited on where you can put them, They can, however, twist the metal that they are attached to, remember, they are not in the middle of a sheet of metal, but on its edge. This makes a big difference in the strength of the metal where these are attached. This type of damage will always cost far more than a single hole used to bolt on an antenna will cost to repair. Larger lip mounts have less of an issue with this as they are gripping more metal and spreads the antennas load out more, so if this is your option, it really does pay to go big with this type of mount. Also, with this type of mount make sure the metal attachment bolts are making it all the way through to bare metal, you need this connection for the antenna to work well
If you refuse to bolt on an antenna, the question becomes 'how you are willing to risk compromising your vehicle?' Only you can answer that question, but if the vehicle is really that important to you, why are you risking compromising it in the first place?
The DB