I think it depends on the league, how it's set up (number of teams, divisions, etc.), it's members...lotta variables that can affect how best to handle each individual situation.
Long Story Short? Discuss it as a league and try to reach a consensus on how to deal with it. If they can't then you'll get the always enjoyable task of making the call (and quite possibly p*****g some people off).
Being a commish can be such