I believe the 1st Amendment's correct intent is to prevent the government from singling out a specific religion (ex. an employer refusing to hire someone because they're Catholic).

It wasn't intended to provide affirmative action for religious people, as in give "religious" people an exclusive right to do certain things which other people can't.

The argument the OP's making is the same argument which has occurred in cases where Muslim women claimed "religious discrimination" for wearing a veil in violation of employee dress code (even though no other women are allowed to cover their face), so it's equally foolish. The Hobby Lobby decision should be modified as well.

Ideally though I'd like to see anti-discrimination laws only apply to larger companies which service a large percentage of the public, not mom and pop stores like this - I don't think that small businesses which can't afford a lawsuit should have to fear going out of business over dubious discrimination claims.

That and I'd like to see putative damages awarded to a charity of the plantiff's choosing rather than the plaintiff themselves - this would cut down on frivolous lawsuits - so yeah I'm happy they got their donation money, because if being offended is worth $135,000 in damages, then anyone who visits 4chan should be a billionaire.