Hey Isham, No, It isn't safe to camp on your own in Thar desert. First thing you will not be allowed to pitch tent in the desert ( hopefully you take Jaiselmar as desert camping place). But you can book Camps in Sam village. And if you have more days in Jaiselmar then book a desert hiking package ( 5 days camel desert safari passing through jungles and no man area; Camping in desert under open sky every night with bonfire and going up to last village on India-Pakistan border). Hope this would help you.
It is a very bad idea. Deserts are not at all a place where you can wander and find something amazing. If you are planning to go in a desert, you must take care of many things. To avoid any risk of this type, it is better to just book with some camp provider.