These two cases are completely different. One is about a non-profit being prohibited from speaking about a candidate before a primary election, and the other is about discrimination by a commercial service.

If a photographer does this, you must choose between political speech and non-discrimination because the political speech interferes with a right of a vulnerable group to enjoy their purchased goods. Otherwise where do you draw the line?

Or what do you do if a cake decorator insists on a similar slogan on the wedding cake and opposite-sex decorations? Surely this is both political speech and functional discrimination, right?

The EFF avoids this by having a narrower focus.

In Citizens United, the ACLU did not take a line which said that for-profit or not-for-profit was relevant so I don't think you can rationalize the line they advocated in retrospect based on facts they argued were irrelevant.

There is a huge issue in anti-discrimination law (regarding the Elaine Photography case) regarding speech as discrimination, and I don't think you can waive away the issues so lightly. Certainly if photography is insufficiently expressive to warrant first amendment protection, I wonder why it is covered under copyright law.... I usually suggest supposing that instead of outright refusing service, if the wedding photographer placed a slogan and logo on every wedding photo along with terms of service that forbid the customer from ever removing it, and which was unfriendly to same-sex couples, (for example "One man. One woman. One holy marriage." emphasizing a religious dimension regarding marriage, and the belief that it is between one man and one woman) if this would be protected. It is clearly political speech in a commercial setting, and it is also clearly discriminatory (in the sense that it would effectively deny same-sex couples a right to enjoyment of their photographs).

If the ACLU is going to take a line that says that speech that is socially harmful is unprotected, maybe they should agree that restrictions on pornography should be up to the legislature if the legislature can show evidence of social harm, but of course they don't. They seem to hold that speech is good, especially political speech, unless it discriminates in ways they don't like, but that is hardly a robust defence of free speech there. The fundamental test of free speech is not whether the accepted viewpoints can be freely accepted, but quite frankly whether the Neonazis can march at Skokie or whether a cake decorator or photographer is going to be compelled to endorse a political message that he or she disagrees deeply with merely because it is a part of a commercial transaction. It is the unpopular views which must be protected.

So I don't think you can have perfect nondiscrimination in a commercial service without saying there is no free speech in the commercial sphere, which is where the case ends up on a collision course with Citizens United and why I wonder if the ACLU draws the line at speech by corporations that gets in the way of their other causes..... (BTW I have a relative, now deceased, who was kicked out of the ACLU for defending first amendment rights more than the ACLU was comfortable with in the 1950's-- he was defending the rights of Communists. They did apologize much later. I would point out that the ACLU has not been exactly a shining beacon of support for the 1st Amendment consistently and this is nothing new.)

Getting back to the EFF, I think they have an easier time because their focus is narrower and so they don't have the issues which get the ACLU (at least arguably correctly) labelled as inconsistent. For this reason, I think that of the two organizations, the EFF is by far the more needed one right now.