... the deflection that should have been 5, nothing going your guys way...
Ah no.
The rule (my capitals) is:
"If the boundary results from an overthrow or from the wilful act of a fielder, the runs scored shall be any runs for penalties awarded to either side, and the allowance for the boundary, AND THE RUNS COMPLETED BY THE BATSMEN, together with the run in progress if they had already crossed at the instant of the throw or act."
and the batsman had completed two runs when the ball crossed the rope for the boundary. So six was correct.
The rule was put in place to prevent the "oops, slipped" four from the last ball of an over that might keep the good batsmen away from the strike, and expose the #11. Old rule, they run a single to keep the good batsmen on strike, "oops, slipped" and it is four, and the #11 gets to face 1st ball of the new over. Current rule, if they have completed one run, or crossed heading for one run, "oops, slipped" and it is five runs and the #11 gets to hid at the non-strikers end again.
You could argue that the subject / object structure of the sentence is ambiguous, but there is a reason the laws are written in simple English rather than legalise. Note the placement of the last comma in the sentence. Note that "if they had already crossed at the instant of the throw or act" is a qualifier for "together with the run in progress", but was not used in the previous part of the sentence.
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Edit - have just rechecked the laws site, there is a line break, not a comma, between "the runs completed by the batsmen, together with the run in progress if they had" and "already crossed at the instant of the throw or act"
which means my earlier comment aboout the comma placement is wrong, and Taufel is right, should have been 5 runs.
https://www.lords.org/mcc/laws/boundaries