The inane part of this second customer's judgment is that, objectively speaking, the gay couple wasn't causing anyone else harm by shopping together in the store. So what was the point of his inherent judgment? (despite the fact that he claimed NOT TO be judging anyone...)

If a gay person tried to physically/sexually force themselves onto another person against that person's will, THAT would be an example of causing harm. But that isn't unique to homosexuality. People of every sexual orientation can be predators or harassers.