The colonials using suicide bombers against the Cylons was not only controversial (even more so now, when it could easily be interpreted as sympathy for the methods of IS), it was a stupid thing to do in-universe.
Earlier in the show, at least one Cylon had done a suicide bombing in a way that made sense: he was probably about to be find out as a Cylon infiltrator and spaced, and by killing himself he would be resurrected anyway so he could as well go out by doing some damage. His position on Galactica (or on the wider fleet) was no longer tenable.
With the remaining colonists however, we see Roslin keeping a scoreboard, recording every death and the odd birth. On New Caprica, suddenly a fair number of colonist don't think that survival of the human race is important anymore and they reduce themselves to being a delivery mechanism for a bomb. And all this to hurt Cylons who are reborn a few hours or days later, while also simultaneously convincing most Cylons that extermination was the right idea after all.
This is all the more surprising considering that the occupation seem to have been the thing they objected so much about, when earlier those people somehow avoided suicide in the totally desperate situation they were in (with them even being chased through jump after jump, early on in the show). When admiral Cain used Pegasus - and the few civilian ships she came across - in what were essentially suicidal attacks, the show seemed to convict her for this. Curious that the total destruction of the colonies (and the death of what, billions?) was no excuse to do what Cain did, but the rough living conditions on New Caprica totally justified suicide bombing.
My impression is that Ron Moore had lost his interest in BSG at that point, and he really wanted to do a story about Iraq so he - inappropriately - pushed Iraq into BSG.
