Resolve that by providing some kind of incentive for how teams finish in their group. I know the league likes to reward the shitty teams but give the 3rd place team in each group so much allocation cash so they their is incentive not to finish last. Although the players might not care about allocation money so maybe something else.
Take our series vs Houston this year. Houston wins the first game 2-0, we win the second game 1-0. So we split the series 1-1, so we head to a 30 minute overtime period and then PKs if need be. It makes both games "independent" of each other. With aggregate scoring it's just one 180 minute game.