It might make more sense to collect all 12 (expensive as that may be). After all, to more casual readers that might buy tpb collections (versus people who, you know, actually follow comic books), how much story would readers feel they're actually getting with just issues #1-6? Wouldn't they be getting more of the questions / teases than any actual resolutions?
It's a 12-issue story, so probably best to collect it that way.
Aside from some fans complaining about it being dishonest, how much of a "fiasco" was Before Watchmen? Did it not sell well?
Were the complaints generally from people who felt DC was just sticking it to Moore again?