In gluten intolerance, our body recognizes gluten as a foreign substance and starts producing antibodies against this protein. Casein has a structure similar to that of gluten. The same antibodies that were produced against gluten sometimes mistakenly identify casein for gluten due to the similarity in their structure and start acting against it. This is known as a cross reaction. When in spite of having a strict gluten free diet a person does not report any improvement in his symptoms he is advised to go dairy free as well just to determine if it is a case of cross-reactivity. However, these people can re-introduce dairy in their diet after sometime.
Ghee by nature is gluten free. However, it may contain some amount of casein which may cause cross-reactions in susceptible individuals. In order to be sure that your ghee is casein free as well, do not over cook it. The moment you notice the bottom residue has started turning light brown continue cooking for a minute and switch off the burner. Carefully strain the ghee into another container making sure none of the residues gets inside the container. However, this residue also contains a lot of ghee. Remember not to try to squeeze out the ghee out of this residue. By doing this you may accidentally end up adding casein to your ghee, in spite of all the precautions that you take. The ghee from the residue can be used for other members at home who are not allergic gluten or casein. The casein or the residue left behind should also not be thrown away as it contains protein and can be mixed with a little sugar and given to kids or mixed with flour to make chapattis or paratha.