They didn't assume that Clark was killed in Afghanistan but missing in action I believe is what Perry said to Lois.
That excuse is flimsy at best. Where did Perry get that assumption? If Clark never was there to begin with, who would report him missing? If no one did, and Perry is just assuming that is where Clark is, wouldn't he want to give a quick call to wherever Clark claimed he was going to be at (at which point, the place would say "Clark who?" or "He never arrived.")