What if the points system always gave 3 points to the winning team, and up to some amount of points (my example below gives a max of 1.2, but this can be changed) for the losing team getting rounds? I think the big flaw of the points system is that a team can get 5 rounds, win, but receive different amounts of points for that win, which stems from the "every match gives out exactly 3 points" mentality, which I think is dumb because not all matches are the same. What if, let's say winning got you 3 points, and rounds on loss got you 0.3 points? So if team A beats team B 5-3, then team A get's 3 points for winning, and team B gets 0.9 points for at least putting up a fight and capping rounds. This would also mean that winning guarantees you 3 points, and it's still worth it to get rounds if you lose, but the spread in points you get from winning and losing is larger than it is now so the "better w/l has less points" is less likely. Depending on how much you value rounds won while losing, you can change the value of how much each of those rounds gets you.
I'm also not against using straight w/l for placement and points or some similar system for tiebreakers, however the points system can be changed to more heavily favor winning.
tl:dr turn 2-1 and 2.5-0.5 win scores into 3-1 and 3-0.5 scores to reward winning more