Rule 2.00 in the official rules of Major League Baseball defines "The League President" as:
THE LEAGUE PRESIDENT is the league official charged with enforcing these Rules, fining or suspending any player, manager, coach or umpire for violation of these Rules, resolving any disputes involving these Rules or determining any protested games.
Rule 2.00 (League President) Comment: With respect to the Major Leagues, the functions of the League President pursuant to these Rules shall be carried out by the designees of the Commissioner of Baseball. The Commissioner may designate different officials to carry out different functions of a League President pursuant to these Rules.
So the Commissioner or his designees would handle anything like that.
Source: MLB rules - http://mlb.mlb.com/mlb/official_info/official_rules/definition_terms_2.jsp
NOTE: Just like in other sports, the MLB rules are designed to be used for all kinds of leagues, not just the professional ones. Minor league teams and club leagues usually follow these rules (mostly) and have their own presidents, hence the use of the term throughout the rules even though the American League and National League no longer have their own presidents.