From what I've read over the past months, it's not just the footballing bodies that might do the most damage, bearing in mind that a European ban is simple enough, because all clubs are 'invited' to compete in the tournaments, clubs have no divine right. Hence why UEFA bent the rules when Liverpool last won the Champions League, and failed to qualify the following year, they were given a wild card because of not having the holders able to contest the following season, and defend their title.
The bigger problem for City will be the financial investigations by law and not footballing body. Charging City's women's team 20 million per year to use the clubs name for example.. most league clubs couldn't afford that, so how does a woman's football team achieve that? Claiming a sellout at every home game, when they are clearly not, the list goes on. Time will tell, and if all is to be believed, the majority of Premier League teams have complained too, not just the 'big clubs', so the situation is getting harder to ignore.