The Cylons probably injured the child so that the bonding would happen.
There are, I think, more allusions to Cylons as America in Iraq, than allusions to Cylons as Islamofascists. For myself, I think our viewing of plot points alluding to the Cylons as Islamofascists is accidental, due to the writers considering the Americans and Booosh as fascists.
It may be well done, but so far this season of "Battlestar Iraq" is annoying the hell out of me for bringing in this not-terribly-well-disguised political crapola.