[nunya bidness]

this could be seen as an allegoric depiction of the islamic goal of dominating all of the Earth, humiliating all non-muslims, and forcing all to submit to Allah and/or the global caliphate.

Without a doubt. Boomer asks the question: Does humanity deserve to live? It's the same question non-Muslims need to ask themselves.

Furthermore, the rise of the so-called "moderate" Cylons, Six and Boomer, seems to have fizzled in the year before the occupation. The same could be said in Islam.

[Question_Assumptions]

I'm expecting the "moderate" Boomer to have another change of heart, which will probably set a new direction for the show after the current arc is resolved. She's not only eventually going to run into the Sharon who thinks she lost her baby but she's going to face the Chief not accepting her and having a baby by the woman who shot her. She's not going to find the friends she's looking for. Six will be more complicated, but if they track with the original Galactica at all, it could end with Baltar with the Cylons.

[antiRepublicrat]

Furthermore, the rise of the so-called "moderate" Cylons, Six and Boomer, seems to have fizzled in the year before the occupation.

My guess is they did have a moderating effect -- subjugation instead of extermination. Still parallels the degrees you see in Islam: kill the infidels, enslave the infidels, tolerate the infidels, respect people of the book.