Can churches who refuse to marry Gay Couples lose their Tax Exempt Status?

No. The case you cite denied tax-exempt status to Bob Jones University because it systematically practiced racial discrimination by refusing to admit students who were involved in inter-racial marriages or who advocated inter-racial romantic relationships. Federal Civil Rights law specifically makes discrimination on the basis of race illegal. There is no Federal law prohibiting discrimination on the basis of sexual orientation, however, so churches can't be stripped of their Federal tax exempt status for refusing to perform same-sex marriage.