Does it seem like a joke that religiously-motivated activists are attempting to legislate the intrusion of a specific religious opinion into public school science education curricula? No, that's not a joke. That's real, and it's important. And to the extent that Bobby's letter, Pastafarianism, and the Flying Spaghetti Monster are part of an effort to clarify the dimensions and implications of that situation in public debate, they're not a joke either.
Or do you mean things like pirate garb, beer volcanoes, and praying to a flying invisible pasta dinner? They might be a joke to some. For others they might be fervent heartfelt beliefs. How are you going to tell which, for whom? That's part of the point too. (The connection between personal freedom of conscience, and intellectually honest scientific inquiry, is fundamental but difficult to explain. Please forgive us if the point comes across as either too subtle, or too heavy-handed.)
As to taken too far... how far is too far?
Far enough to offend someone's deity? Any deity that takes offense at the content of this site is welcome to contact me in any of the myriad ways its defic powers must make possible. I would greatly welcome such contact. I'm sure most others here, including those in charge, would say the same.
Far enough to offend some other person on behalf of their deity? Ah, that I can't bring myself to worry about. First, if their deity is powerful enough to fear offending, then he/she/it should be able to take care of him/her/itself (see the previous paragraph). Second, I cannot possibly avoid offending people on behalf of their respective deities while living any sort of recognizable modern life. I do so every time I permit my wife to leave the house without her face covered, practically every time I eat a meal, and most of all, every time I worship my own deity of choice.
Far enough to trivialize, marginalize, or mock other people for their beliefs? Yes, that would indeed be too far. Which is why it's strictly against policy here to do so, except in specific forums which are clearly marked as open to such content and which those who want to avoid the risk of offense can easily avoid.
So on what basis could one say that the subject matter of this site has been taken "too far?" If the above hasn't answered your question, perhaps you could clarify that point, as the basis for further discourse.