I already asked the WMs to change/edit the rules for this. If I were WM, I would have them state something like the following:
"You must not edit your vault (decks, salvage, discard, etc.) after the deckbuilding period ends. If an edit to the vault after the deadline is to be made, it must be approved by WMs. The exact penalty will be at the discretion of the WMs. Edits made shortly after the deadline will be weighted much lighter, as is notifying WMs of late vault completion. Any part of a deck (card, upgrade, or mark) may not be edited after a match has started. Any edits to a deck must be approved by a WM prior to starting the match."
In general, when I was a WM I would only allow edits shortly after the deadline. Probably the only exception being for very minor "obvious" edits (like a wrong mark) I would allow mid/late round prior to starting the match.
I'm sure people would have slight modifications to what i wrote above, but i think it clarifies these situations a little more clearly yet gives the WMs flexibility in handing out penalties.
Personally, I prefer adherence to strict rules during large events like this. I remember when Kael Hate was WM and he handed out penalties for not having the title in a battle thread being perfect. I'm not that harsh, but the rules need to be clear so that it can prevent stupid drama like this.