I think the reason people get so angry about season six/seven (concerning the supernatural aspect of the show) is because this good versus evil thing pops up, and it leaves no question unanswered, no blanks to fill. Up until then you had plenty shades of grey, but it all stopped right there- the Prophets and Bajorans are good, in fact Sisko and the gang are the "good guys". The baddies are so bad it makes one's brain bleed (thank you Virginia Woolf for the use of that particular pronoun).
No ambiguities, that's what I'm trying to say. They had been there, but eventually, they vanished. We got told explicitly who's good and who's bad.