More seriously, an infinitely better option is to express anger and disappointment with politicians who would seek to use their positions of representative power to limit free enterprise for a completely unjustified reason.
If you dislike that the CEO of Chic-Fil-A thinks homosexuality is immoral, thinks that Gay Marriage is going to bring God's wrath down on America, and donates extensively to related right-wing causes, I think it is perfectly legitimate to agitate for a boycott, because it gives the opportunity for each autonomous individual to speak with their money and deny funding to things they oppose.
If you are really concerned about donations from wealthy corporations helping to determine court cases and legislation that affect people's rights in an anit-Democratic fashion, agitate against THAT, don't undermine free speech and due process by attacking someone taking advantage of the system, which is truly the problem.
On the other hand, this nonsense from Rahm Emmanuelle about denying building permits to the chain because of its discrimination is a terrible response. Firstly because it usurps the individual's democratic right in society from getting to determine their own feelings about the issue, but also because it is obviously not discriminatory in any legal or relevant sense. Chic-Fil-A the restaurant serves all people equally, hires all people equally, doesn't use any hate speech in its marketing or anything, and conforms to all relevant laws I am aware of.