Can you point out in the rules where it says that two fouls equates to a second booking because the first one was a bad one? Probably not, because it doesn't say that anywhere, it's just what you want the ref to have done, rather than what they are obliged to do. Agreed on the tightrope assessment, it was good management to get him off the pitch before the ref did.
I get the frustration because of the impact to the result itself and also to Bentancur's season, I do think a yellow card isn't a good enough punishment but also don't really know how you'd go about making it "fair". Even if it was a red (which I don't think it should have been) it doesn't undo the damage to the recipient of the challenge's well-being nor the team.