Personally, I think the reason these guys tried to coverup what they had done is because they knew that what they had just done was illegal. That is the only reason I can think of as to why they would have "panicked" in the first place. From what I have learned, B.P. agents have cause to fire their weapons often throughout the year, and some of those situations have ended with the suspect being killed. And yet none of those B.P. agents faced charges nor reprimands, etc., because they followed the law and the procedures in place for reporting such events.
You said, "How hard would it have been for t hem to say he had a gun in his pants and turned to fire? Who would have known the difference?" Yes, I suppose if they could have come up with a better lie. However, is that what we want our law enforcement officers to do? Become good liars?
These two agents had a reason for getting rid of the evidence. That fact alone should speak volumes.
After what happened to the Pendleton 8 for doing their job and given the Presidnet's de facto amnesty position on illegal immigration, I can see why tehy might well panic after doign exactly what they're supposed to do.