You make a good point in general, but this particular case is about preventing non-scientologists from treating the 'religious object' devices how they will, not about the scientologists being at all restricted in their own handling of the objects (as would be comparable to illegal drugs or animal sacrifice used in religious rituals).

This case in particular is comparable to requesting that the government outlaw the modification or destruction of the Bible or Qoran, even by people who own their own copy of a religious text. It would require non-adherants to a religion to treat that religion's objects as sacred and to do so in the specific manner prescribed by that religion. This is contrary to precedent and law established by cases against people who've burnt their own personal copies of the bible, or created derivative works making fun of the bible, and so on.