Take the same scenario as the OP, where one player is locked out of top 8, and the other player can make it with a win.
What if the locked out player doesn't just scoop or concede at the outset of the match, but actually plays the match, "wins" the match, and then scoops? Does that make a difference?
Chubby Rain scooped Jazza into the 6/17 top 8, after he beat him, and then Jazza went on to win a tournament he otherwise would not have won. That's not just harmful to the person who was left out of the top 8, but all of the other players Jazza beat.
I don't know that I have an answer here, but I do think that those comparing MTGO to paper magic are making a mistake. The rules of paper tournament magic and MTGO are different. The fact that you can't ID on MTGO and you have a clock fundamentally changes the game. People are able to manipulate the tournament structure to their advantage by drawing intentionally, but can't do that on MTGO. To me, that makes MTGO a different beast.
In a Pro Tour, you can ID in the last round so that both players make Top 8. You can'd do that on MTGO.
I don't think you can legislate players not to scoop in friends of teammates into a top 8, especially if they are locked out. But I don't think that ends the matter. If there is an implicit expectation of reciprocity down the line, that could be an ethical problem. " I scoop to you this time, and you scoop to me next time," even if there is no definite guarantee that will happen. That could an ethical problem, even if it's not a rule violation.
Not all ethical rules are legislated.
I see this more as a gray area than a bright line rule, because there are different circumstances that warrant different ethical analysis. But there are real ethical concerns here that shouldn't be papered over.