I don't think the pheromones are all that stupid. Humans have them...but we're not always aware that they're working on us. Human men secrete a musky smell (I don't mean stink) that is meant to attract women. This smell also repels other men. Humans wear so much deodorizers that the smell isn't as strong as it used to. Pheromones can be seen at work constantly in nature all around us. Many types of female animals secrete a pheromone when they're in estrus which drives the males crazy. Male elephants go through their own type of estrus, where they're uncontrollable because their need to procreate is so great...I think it's called Musth. But pheromones aren't stupid. They exist and they're a reality.
I don't think that the intention was to deny their existence, but rather that their use in fiction overstates the effect they have on human behavior. Indeed, pheromones are a whole field of secretions that can affect many aspects of social behavior, not just sexuality. The problem I have is that pheromones are often only presented in terms of their potential for arousing, in contradiction to the fact that pheromones play less of a role in human individual and social behavior than in other animals. Moreover, those pheromones are species specific. Of course, this is what makes the OP's question interesting: is there a biochemical so powerful that it can overcome not just differences of species and sexual orientation, but also a whole field of personal preferences and attitudes toward sexuality, both personal and cultural.