There are three different matters we should differentiate:
1) Activity Levels:
I don't want to do that all over again. I don't care about losing characters, or losing a war in BM. I do care about losing a war when, as stated by Anaris before, clans have a 1.5x-2x advantage on your average realm.
That, to me at least, goes against the "Fair Play" section of the Social Contract.
Sorry, but this is basically you saying "Oh no! They are too many and too active, they should accommodate to our speed of playing!". Sorry, but they should not, if you want to play it slow and still win then go to the Colonies, in where there is only one turn per day, or advocate for a larger island with that pace. It makes as much sense that you have the same right to play at a slow pace than that you have the right to be extremely active. And this comes from someone who couldn't care less about the military aspect of the game.
If you don't have time to wage a war and win it then you should not be focusing on that, specially if you don't have enough nobles in your realm.
2) OoC Friendships:
My chars generally support these families because they know that the favor would be returned someday, without prompting, promises, or even a formal acknowledgement of mutual assistance.
No offense, but I personally consider this of poor taste. Not a crime, nor something that should be punished, but certainly something I would try to avoid. It makes one think all those characters are extensions of the player, without individual goals, dealing with extensions of the other players.
But that is also associated with the objective one has in mind. If what you seek is military and political victories with all of them, winning in general, then it makes sense. I try to have different levels of ambition and trustworthiness in my characters, and different goals. I would certainly not recommend a good friend of one character to necessarily trust the other, for they might find a nasty surprise. And that is one thing I like about BM's social game: the uncertainty.
3) Clans:
That depends. Three people with two characters apiece could easily control the government, dukedoms, and armies of a small or even medium-sized realm.
People who play in a group become a problem when they actively exclude others from that group. If you can't get a leadership position in your realm because you don't belong to the OOC cabal that runs everything, that's bad. But I'm not sure how exactly you'd distinguish that from the IC cabals that naturally form as people play together for years.
Indeed, there are two factors to consider, size of the group and level of OoC friendship.
A clan of only 3 players and 6 characters should not be a major concern, in my opinion. There are much worse IC cliques around. If six players decide to make six characters run around as the biggest buddies, I have no problem with that. It can be considered a clan, but it's of little impact. Why cannot RL friends not play together as friends IC? But if they decide to make all of their characters as the biggest buddies, in a short time in the game summing up between twelve and eighteen nobles that always share the same realms and work at a group level... Well, then they are creating problems, and should try to play with people outside their bubbles.