From the article:  "For florists and bakeries, should the exemption only cover same-sex weddings and not other purchases? Should exemptions for religious institutions cover all employees, including janitors, or only those considered 'ministers' and teachers of religion? 

Good questions, but....  
1) Florists and bakers should have no exemptions regarding baking a standard wedding cake or providing standard flowers for a lgbt wedding.  Whatever they would have done for a straight wedding they should do for a lgbt wedding.
2) Core religious institutions where faith is taught and practiced can "discriminate" when it comes to "ministers" and "teachers of religion," - the parish office, the diocesan offices.  Religious affiliated institutions, such as hospitals or universities, that serve the public and receive any form of government payments or subsidy, cannot discriminate in employment or the public they serve or in the health insurance they provide to those who work for them.