The AF had little to do with the Eurasia's problems. The actions of destroy was the actions of Logos. Go to gundam official and look. The AF never invaded or occupied any part of Eurasia. Zaft was fighting Eurasian Gov't troops. Remember that phantom pain is not an official part of the EA.
You are placing too much blame on the AF for the Actions of the Eurasian Gov't. The middle eastern thing was Eurasian. the only AF ship to fight in any part of Eurasia is the Jones. The AF would never name one of there ship the Bonaparte.
Western Eurasia was in Full revolt. !!!!!!
I don't remember Gundam Official specifically mentioning ZAFT fighting Eurasian troops on the Mediterranean Front, especially when Suez Base is a de facto AF base. Phantom Pain is LOGOS' militant wing as well as Alliance black ops forces. It doesn't matter if they're part of or not part of the Alliance. The fact is they are Alliance forces through and through, as shown by the reactions of the DSSD staff when Phantom Pain announces their presence to them. The Middle Eastern uprising is part of the general Western Eurasian revolt. The Jones and Bonaparte are both Phantom Pain, and by extension, AF ships. True, the AF would never name a ship Bonaparte, but remember that Phantom Pain has special powers allowing it to requisition any military asset it deems fit to conduct operations.
Allow me to raise several points missed in this discussion. Why should i demonize the AF? Because it is clear they are the most heavily infiltrated faction by Blue Cosmos/LOGOS. Evidence abound, including but not limited to:
1) The Alliance nuclear assault force attacking PLANT with nukes in early GSD hail from Arzachel Lunar Base, which is seen later in the series to specifically be the Atlantic main space base due to their President relocating there after Durandal proclaims the Destiny Plan.
2) The Azrael Conglomerate and other LOGOS corporations are deeply rooted in the Atlantic Federation. It was the Atlantic Federation which attacked Orb in Seed, and their AC-built 2nd-gen Gundams played a major role in the war from that point onwards.
3) Again, the Atlantic Federation practically forces every Earth-based faction to join the Alliance except for the Oceania Union. That fleet blocking Minerva at Orb belongs to the AF.
4) Djibril is seen specifically ordering President Joseph Copland to pacify Western Eurasia at least twice, and those MS squadrons seen occupying Western Eurasian settlements are implied to be from the Atlantic Federation. And since he is also the one ordering the Destroy to rampage across Western Europe and the de facto leader of the AF, whose armed forces have been shown time and again to have plenty of people screaming stuff like "Die all Coordinators!" and "For a blue and pure world!" i can safely say the Atlantic Federation is a LOGOS puppet state and also the one sending all the MS battalions to pacify Western Eurasia.
5) This is not the first time the AF has deliberately do something nasty to the Eurasians, as exemplified by them ratting out their Eurasian comrades in JOSH-A. Given the circumstances, they would have no compunctions slaughtering innocent Eurasian civilians.
Does that satisfy you, Lordyu?