I'd say if the MLS is willing to be distracted, it should be distracted by giant revenue producers like these big-name friendlies. Professional sports is a race for money. That is the north star. Having a team that never won anything to even get into the competition flying down to play Isidro Metapan in the thick of the playoff race for a game that won't be on TV in a tournament that won't be resolved until the next season is not a big revenue potential idea. The Champions Cup, when it was a brief, circumscribed tournament for teams that had actually won something, made more sense and was at least less harmful. The new format is based on the idea of "more teams and more games is better! We should be like the European Champions League!". That's wrong and in service of no one's interests, and MLS should not feel obligated to be a part of it.
Distractions (and money-making exhibitions, etc.) would seem to work better (for all involved) if they were solely placed in the off-season or pre-season (or mid-season break) periods. But yes, the "nastiness" and realities of business will always encroach on "purity" of real competition-focused concerns for MLS/SUM (and the clubs they'll host and with whom they'll want to do business).
Decertified? Like, the USSF take away our D1 Sanctioning? Not gonna happen, because the USSF needs MLS' money. Or like FIFA taking away the USSF's sanctioning power? Not going to happen, because FIFA needs USSF's money. Something else? Not currently possible under FIFA rules.