You have a good point about how the general public can be their own worst enemy, but I can't help but feel that Disney was asking for this scenario to play out in the that way it did no matter how hard they tried to avoid it. They may have treated the attraction with maturity, but as I said, those efforts can only go so far when you're dealing with an experience that is completely subversive in the context of where it is being presented.
Thrilling, but not exclusively adult, attractions such as Space Mountain may not be everyone's cup of tea, but they are expected and don't straight up undermine what the Magic Kingdom's identity is or is percieved to be. Yes, it's important for Disney to take risks and go beyond what is expected of them, but it's also important that they don't go too far and end up achieving the opposite.
To be clear, this isn't to say that Disney shouldn't create experiences for demographics they aren't traditionally associated because they most certainly need to do so. In fact, that's the beauty of having 4 unique parks with different overall themes, tones, expectations, and, to some extent, audiences. If put in a different park, an attraction like Alien Encounter may have the opportunity to thrive. But because it was where it was, it was met with controversy that wouldn't have been remedied by simply reading signs. Just because something is read doesn't mean something is accepted.