There is a huge difference between "skunk in right field" (which is intentional and does not involve the baserunner abandoning the bases) and walking off the base toward a dugout thinking the play is over (which DOES involve abandonment).
I think I call this kid out too (althought obviously HTBT). The removal of the helmet is an added clue into the fact that the runner had abandoned his base.
Now, regarding your true question in a more general sense...
If a rule is misinterpreted, the umpires must confer and fix the situation, including placing runners where they should go. Let's change your scenario a bit, leaving the runners helmet on, and having him touching 3rd, and then walking directly down the baseline toward home. Now if coach yells at him to run home, and U2 calls him out, you MUST confer and decide where to put the runner. Likely, I'm putting the runner at third base, 2 outs. (And, as noted above, defense would still be able to appeal his leaving 2B early!). Once U2 called the runner out, you can't call him safe and keep playing, so you essentially have a dead ball scenario, during which you "fix" the situation.
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