It's really hard to tell how much damage the Freedom sustained at the end of SEED1, it seems Kira got blown out of the cockpit by the explosion of GENESIS... that means the Freedom should be pretty much completely destroyed. But it seems Kira is totally fine and there's no single scratch on his suit... so maybe Freedom didn't got damaged much but just some auto-eject got triggered to eject Kira out... Still to eject a pilot with nothing but his pilot suit is a bit ridiculous... I guess those guys just didn't finish building the proper auto-eject mechanism for Freedom back then
