In my opinion, this would still be fairer than if Vasya, who didn't even guess the outcome of the match, received the same number of points, or even more, as Petya. Penalties are essentially a lottery; they are held because it's much more interesting for the audience than flipping a coin.
Why invent something I didn't suggest?
According to my proposal, Vasya will only receive 1 point for progressing past Uruguay, not "2-3 or even more than Petya."
As for the penalty shootout being a lottery, that's just a figurative comparison. It's still not completely random. Compared to regular time, penalties are like poker versus chess. But who said there aren't strong and weak players in poker? The strongest team simply doesn't have a total advantage, but it still exists.