So, for capital crimes, relying on people's judgement is ok, but not for money matters? I think your priorities may be a bit screwed up.
The simple fact is that the government is already making those judgements. As someone who has founded three religions (one of which had as many as five members at one point), I assure you my ability to write off church expenses is precisely nil.
I agree, "common sense" is not sufficient by itself for such matters, but since these judgements are already being made (see my earlier reference to the Mormons), why can't they be applied to Scientology? I don't know the gory details, but I'm pretty sure the criteria for becoming a tax-deductable church are rather more complicated than "just some guy who decides". I'm pretty sure there are laws and precedence.
If some random guy (like me) could just declare himself a church and stop paying taxes, and the government weren't allowed to decide whether that's a valid claim (as OP seems to think), I'm pretty sure the amount of taxes collected in this country would be pretty close to zero!