My analysis of it is that neither "that" nor "it" belongs in the sentence, and neither does the comma.
Usually when you use the "just because X does not mean Y" construct, the "X" part is so long that there's the desire to stick in a "that" or an "it" to reiterate that you're referring back to an actual noun. Otherwise it feels like the back half of the sentence floats without a noun. Note also that the comma doesn't belong there either: That's a verbal tic, a pause for breath, not a grammatical construct.
(EDIT: Just to be clear on this, I think both the "that/it" and the comma are the result of writing as though the writer were speaking. In speech it might feel necessary to breathe and then restart the half-completed sentence with "that" so that you have a subject noun.)
However, just because the forward part of the "just because...does not mean" sentence is so ridiculously long and convoluted that nobody in their right mind could ever possibly follow it and still have the original piece of the structure in their heads does not mean that people can't actually follow it if they're accustomed to the "does not mean" tag on the end.
As a caveat, I'm not really sure how the grammar fits together for this kind of construct. If I were trying to produce something in idealized English grammar, I think I'd say "X may be true, but that does not mean that Y is also true". In a case like that, the "that" is clearly needed as the subject noun of "does not mean".