I was thinking about this and I think I found a little bit of a solution for MLS teams to be able to compete in the league as well as CONCACAF.

For teams in the CL, have them play each other in league play for the first month of the season as much as possible. That way they can virtually both play B teams against each other) and no one is giving up points for free. With 5 teams in CL, it leaves one team out per week, but at least you can say that 4 of your first 5 games will be against teams competing in Champions League (or at least were supposed to be in the CL). It isn't perfect, but it at least should help. The only thing now is it leaves a team like Toronto who didn't advance to have an advantage by playing teams that are still in CONCACAF, but that only affects a game or two