Great question — answering as the UphillTech team:
Cleary was one of the wrongdoers as well. He ”lost” his gun to the suspect — it was a murder attempt to get rid of Tom. Cover up from bad guys, for this was to give Tom a medal for bravery. So it was either him or Wally, and the most logical to the film — it was Cleary, because he visited Eli earlier on, as you pointed out.
Full answer by Dipdap: https://movies.stackexchange.com/a/121763 (CC BY-SA 4.0).
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