Firstly: Sorry I was not able to find out anything about the problems of Starship Traders...
To the post:
I honestly do not see that problem.
I see two possible cases:
a) A couple of players group together for their mutual benefit and score pushing / stats padding.
--> This can neither be avoided with or without official clans.
b) A couple of players group together in a clan to not only push their own score but also that of the clan for fame and glory in the clan ranking.
--> A clan would fight another clan, organize tournaments, private rounds etc. to battle out their own clan leader or the supreme clan of them all.
--> Players are marked as belonging to a clan.
--> Other players may choose to play games with only 1/2 members per clan allowed or they play as they want.
I believe, that only in scenario b) players have the information ready who is allied with whom.
If the clan players somehow have secret alliances with other players, those players will a) not add to their clan ranking and b), we would have the same situation as without clans, namely secret alliances between organized groups of players that cannot be avoided by others.
People who try to get around "the limitation" would do exactly what people do now and they would miss the possibility to really join their efforts and show officially, that they can rule the game.
So sorry, but I still don't see the problem.
(unless you simply don't like clans

)