Interesting thoughts all around. See, I don't think the merger would be peaceful... though it does depend on the world. The primary problem I see is political: the pacifistic forces in the OA are powerful politically, and have not enjoyed the military build up of the Alliance, even in the face of increased pirate aggression.
Where I see it working is on the planets most impacted by pirates. A Clan Snow Raven cluster wipes out a bunch of pirates calmly and efficiently and smiles politely at the local folks and says "Sorry for the mess, have a nice day." I can see the local people going "Well now, those Raven types might be a tad strange, but they okay folks." And the other two flannel wearing Maine residents will nod and go "Ayup." Sorry, I live near Maine so I have to make fun of them once in a while! :)
Anywho, in terms of the Dark Ages after the Alliance is fully going.. true, we don't know much and I haven't really seen any DETAILED maps, though I might go looking for some at my FLGS, however, I see the Raven touman being a powerful check, even after the Jihad. Without knowing how their forces are spread out, and only knowing that at some point the Alliance picked a fight with the Dragon, we can speculate either way. However, I am thinking that the Ravens, being great scavengers, and the Alliance side, being used to working with poor and outdated equipment, will be able to combine their skill sets into one powerful military force in the Dark Ages period.