But I don't think you have a moral duty to boycott Chick-Fil-A (or, say, prevent them from opening in Boston). If you want to boycott Chick-Fil-A, or it makes you uncomfortable to eat there, then sure, go ahead. But it's not like Chick-Fil-A is the Westboro Baptist Church. And I guess I have an allergic reaction to overly politicizing everyday life. Society is polarized enough already - I don't want to live in a world where Republicans and Democrats can't even eat at the same restaurants based on their political affiliations!
A reasonable middle ground - eat at Chick-Fil-A, and donate money to the Human Rights Campaign to offset whatever small percentage of your money goes to anti-gay organizations.