Define "stop". FIFA has powers to penalise them, but it can't literally prevent them from playing the matches. For instance, FIFA can threaten that any player who plays in the matches will be removed from the list of FIFA-registered players, which means they would be unable to play in any FIFA-affiliated league, which would essentially end their careers as it would be unlikely that they'd want to hang around in a league where only banned players can play. FIFA could also levy heavy penalties against the clubs from those countries, such as expulsion from international tournaments (i.e. Champions League etc), banning them from transferring players from other leagues and so on. It could wreck football in those countries.
To break away from FIFA would require enough major countries to be signed up to it that viable national leagues could still be kept going - i.e. if England, Germany, Spain, Argentina, Italy all joined then all players from those countries could play in each others' leagues, and that should be enough to ensure a high quality of football, thus keeping the players on board and ultimately encouraging further defections.
The problem is, while individual FAs may have reservations about FIFA, none of them are anywhere near contemplating leaving FIFA, so persuading not one FA but a whole network of Football Associations to do so simultaneously is not going to happen any time soon.
