Natarle didn't deserve to die like that, but Azrael had it coming. The guy wanted all Coordinators to die, much like Patrick Zala wanted all Naturals to die.
I always come back to this scene, despite having watched several Gundam shows this scene, this episode itself is the one that has stuck with me the most, such a masterful portrayal of hatred, political machinations, the horrors of war and even love, this is the exact moment where SEED went from being just an above average outliner and became a masterpiece, and with that, my favorite Gundam iteration in the whole franchise