Not a word about the religious motives of this action in this article.
Mixed religion marriages are not socially accepted in India. When born a Hindu, one stays Hindu. Converting to Islam and marrying a Muslim is frowned upon (not sure, but I think it is even illegal in a couple of states). So the solution for such couples was to move cities and live together without officially marrying. With this registration, Uttarakand tries to stop that as well.