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I would guess that he didn't consider it, and the military has it somewhere-- which is scary as anything.
I just don't know. I could completely see Clark not thinking about it, but what about Lois - she's there, too. But maybe she wouldn't think of it, either. She's had a busy day, and she's not used to thinking in those terms yet, of aliens existing, etc. It's relatively new. In any event, if they wanted to use it, it could totally be used in a sequel.

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And if Clark did get rid of the body, there'd be some other frightening implications there-- the guilt for one thing.
I don't know if there'd be guilt for disposing of the body, depending on how he did it. Burial is common here (in ice?), but cremation is not unusual, and he could maybe be okay with that. He could try saying a few words, but that'd probably make him feel dishonest/hypocritical, since he killed the guy. But knowing Clark, you're probably right and he'd feel like he was treating the body like trash to be disposed of.

Side note: timeline question? My thought was that Lois came immediately back to Metropolis (after being saved by "Joe"), wrote the story, then tracked down Clark in a matter of days, at most. Others seem to think it took her months to track it down. And she didn't really seem to be injured later in the movie. Thoughts?