@Niagara1864 is in a difficult spot. The account given in the Ball genealogy states that it is only a story; it's been my experience that there usually is often germ of truth in family stories--but how inclusive that truth is in this story can only be guessed. There is a degree of official documentation: the US Register of Civil War Deaths for New York does state that Sam. Owen (of Porter, NY) was killed by a civilian on June 12th. So he has a fullish, but undocumented account vs. a scanty official account. There is also an even scantier 2nd official record:
NARA's
Burial Registers of Military Posts and National Cemeteries also gives his death date as June 12, 1864 but says only that he was killed. Interestingly, there may have been another soldier (same regt., same date of death and buried in the same cemetery in an adjoining plot); this soldier isn't named--just called "unknown".
Given what the rolls of the Provost Marshall contain for the time period, it is possible--but unlikely--that there is a reference. Unless Mr. Ball submitted a claim for compensation after the war's end. But, to tie up that end, I agree that he might contact NARA. The full pension record probably isn't going to be useful--although this isn't definite: pension records are heavy on medical conditions, not social ones.
It appears to me that destroying someone's garden during a military occupation probably involved more than one individual soldier. If two soldiers died in this incident, it seems unlikely that a farmer could have dispatched two armed soldiers--unless he shot from hiding (therefore, there wouldn't have been any conversation). Was the soldier(s) absent without leave or acting under orders?
If Niagara's conclusion is shaky (based on 2 pieces of skimpy official documents), Archie Clement's is also (based on an undocumented summary family story).
My guess is that this is one of many incidents of that time that are unfathomable. There's something screwy about the Ball family story that bears investigation. If I were working on this for my local soldiers project, I'd follow up with
@Story's suggestions to rule out Archie Clement's supposition.