The Federation provides help and assistance when necessary, part of the mission profile of a Federation Starship.
Even Picard admits that Dougherty got the Federation involved in a blood feud. At the point they found out that the S'ona/Ba'ku were the same race fighting for control of resources, the Federation (Picard/Dougherty) should've recused itself from the whole mess. It would, by definition, be an internal matter (per Redemption
The above works under the assumption that the planet does not belong to the Federation.