A protest of anti-gay marriage laws would assume that states have set out laws strictly against gay marriage. This hasn't been the case in America. The gay marriage protests are centered around the definition of marriage which has been considered between a man and a woman up until recently. Therefore the first part of the question makes it really difficult to answer since it doesn't make much sense.
The ACLU has been known to come to the defense of the minority and the oppressed. They claim they exist because "Freedom Can't protect itself." Shouldn't the freedom for a homosexual couple getting married be included in that? The freedom of a gay couple to perform the act of marriage and expect all the same government allotments as a straight couple is guaranteed by the fourteenth amendment. The ACLU views are consistent with gay rights.
The American Civil Liberties Union should definitely be protesting anti gay marriage laws because it seeks to provide support for those seeking freedom anywhere in the United States. This cause falls within their realm of interest because gay people are being denied the freedom that other people take for granted.
Yes, the protest of anti-gay marriage laws is consistent with the American Civil Liberties Union foundation, because they usually take the side of the person who wants the most offensive behavior. The ACLU wants to allow people to do whatever they want in society, regardless of morals or harm to others. So it makes sense that they would protest someone else's protest.
The American Civil Liberties Union should fight to stop the persecution of everybody - not just the rights that they agree with or that they find palatable themselves. Still, the anti-gay legislation stops people from marrying without helping anyone, so it should be fighting against them, unless it forces people to do something in favor of marriage.