From your article...<quoted text>
"Legal action A might not be that bad, for instance because giving same-sex couples marriage licenses doesn’t hurt anyone else. But taking 'action A' will increase the likelihood of legal 'action B', which would be worse—from the perspective of some observers—because it would interfere with the free choice of people or groups who oppose homosexuality."
Exchange the words "giving same-sex couples marriage licenses" with the words "giving African Americans equal rights". Also exchange the words "groups who opposed homosexuality" with the words "groups who oppose equal rights for blacks".
Exchange these same sets of words with "giving women the rights to vote and own property" and "groups who oppose equal rights for women".
Certainly even you can see that refusing to give rights to minorities based on other's rights to oppose certain minorities, sets up a disastrous situation.
Everybody has the right to dislike others based on their own personal belief system. However, folks don't have the right to enforce laws based on those rights--especially when the minority group has NO ILL EFFECTS on greater society.
"Ill effects" or "damaging effects" are the only reasons that societies should be able to oppose certain groups.
Simply "not liking" a particular group is not an adequate reason for puffing unequal and discriminatory laws into place.
The KKK and White Power organizations can exists all they want. But in this country, their opinions about racial, religious, and sexual minorities ARE NOT a basis on which to create discriminatory laws.