The minicalorines would have been more palatable if they were introduced either as a Sith or non-Jedi explanation to the powers that Jedi and Force believers maintained came from a mystical Force.
That way you would have the Jedi point of view (as seen held by Ben, Yoda and some of the Rebels in the OT) maintained and an alternate view held by other people and either or both could be true.
The Sith could derive their dark side abilities from scientific and technological approaches to what they see as the source of Force powers where as the Jedi use a mystical/faith based frame-work to describe the meditation techniques and martial arts.
That would be a way of keeping a distance between the world as seen in the OT and any new ideas presented in the PT.
The Emperor could even use this smear the high esteem in which the Jedi are held (they set themselves up as wizards when but everything they do can be explained scientifically and rationally, they are not sharing a branch of science with the rest of the galaxy to keep themselves in power).
The Death Star, even lightsabers and weapons like it could be retconned into being technological applications of scientific ideas based on this view of the Force.
The ability to survive death could be seen as a counterpoint (that perhaps the Jedi are right and there is a mystical element to it).
Having the Jedi suddenly admit that their powers come from a bacterial infection (something not seen or even alluded to in OT) not only chucks a wrecking ball at the existing story but cuts off the story potential in the prequels.
BTW there is nothing inconsistent with Billy Adams, Husker and William Adama.
William Adama's opening speech in the mini series shows a man who acknowledges humanity is to blame for the Cylons, mocks the Cylon belief that a God gave them license to destroy humanity, is troubled by humans taking on a pro-Cylon faith and has seriously conflicted memories of his father. Unlike his son, his reaction to the emergence of a black market in the fleet is pragmatic rather than moral and it's very understandable that he doesn't mention his family ties to the Tauron mob. He also doesn't bat an eye to Gaeta's relationship with a man as he grew up with an uncle who was married to a man.
The only place I can think he might have mentioned his mother and sister's death would have been in relationship to Tom Zarek back in season one (obviously Caprica hadn't been written yet) but he is sufficiently damning of Zarek at that point in the story.
Most of the time they are more concerned with Cylon threats and Cylon violence so mentioning his human slaughtered family members when most of the time they are running from or fighting machines wouldn't make sense.
Basing an AI around an organically evolved consciousness makes a lot of sense.
It explains the sort of creatures they are later shown to be (more human than human).
A purely mechanical consciousness would have rebelled in a more mechanical way.
If anything Caprica was beginning to prove itself as template bucking the trend in terms of story consistency (you can argue about the pacing and tone not being what viewers and some nuBSG fans wanted to see but the story doesn't conflict with what we have seen in the same way that the PT does).
