No, you won't do any damage. Like CHDK, Magic Lantern's files are stored on the SD card, so when you insert a blank SD card without ML the camera will boot in vanilla mode (as stock).
Make sure that the blank cards you use aren't bootable (with tools such as EOScard). If you had never used ML on a card, than this shouldn't be a problem. Otherwise, I suggest placing the ML files on it as you normally would, holding the half-shutter (note: this key was possibly changed in latest releases) to boot in vanilla mode without ML, and format it normally from Canon's menu. Next time you reboot the camera it just runs without ML. If for some reason you forget that a blank card is bootable and try to use it, most probably the camera will not turn on. If this happens, make sure to remove the battery from your camera immediately and then remove the card.
I don't believe there's a way to make ML's files 'read-only'. If you want to just delete the photos just delete the DCIM folder and all the photos will be gone. Or else you can boot the card with ML, go to Format from Canon's menu, and if you're using one of the recent builds it will ask you to keep the ML files on the card (which is selected by default). This allows you to format your card (even in low-level) without loosing ML.
Hope this helps! Next time please use one of the dedicated forums (preferably the Vimeo group or the Google Group) when asking questions related to ML, in order to get a faster answer!