Buckle up. Long post coming.
I think cancelling the hand is not the right thing to do. Doing so is equivalent to a misdeal, which clearly did not happen. However, since both players were OK with it, so am I - assuming that the 'heads up' you mentioned meant the final two players in the tournament, not merely the only two players in the hand.
I also think your final idea of "Leave the first two cards of the flop and scramble the rest" is wrong for several reasons.
A solution you didn't mention, but might have considered, would be to take all nine cards, and reshuffle them into the stub and put out an entirely new board. I'm against that solution as well.
Several things to consider.
On a four card flop, in Rule 39, we ignore the possibility of 'knowing' which two are intended to be part of the flop, and scramble all four.
Similarly in Rule 39, a flop without a burn gets all three scrambled, with one card removed for the burn.
So, based on that, I'd take all nine cards, scramble them, and put out a new board with burns and one card left over.
Except in the no burn part of Rule 39, it says if there is any action, including a check, the flop stands.
But the players were all in pre-flop. What 'action' could there have been?
Last, Rule 38 and Procedure 14 says burn cards are to protect the stub, and NOT to 'preserve the order'. I.E. Random is random.
In other words, the cards that were face up were just as randomly likely to be the actual board as the 'intended' board cards, and therefore the hand should stand. That's the way I would have ruled.
OK. Maybe that long post wasn't as long as some of my other posts.