It's not clanning because Secret Societies are an official, in-game mechanic. Secret societies are things that can be discovered, infiltrated, exposed, etc., all completely IC. Membership in it does not depend on an OOC relationship.
Now, it is perfectly possible for a clan to use a secret society, or for membership in a secret to be restricted based on OOG clan affiliation. That would also be against the Social Contract.
The difference is between OOG and IG. If promotion, membership, power, voting, etc. are based on OOG affiliation rather than IG affiliation, then chances are there's a clan involved.