Sanji should be feared by the World Government. But not as a fighter.
Strong in his own right he should still be quite a bit weaker than Luffy and Zoro. The role of Sanji should be a strategic one that ends up causing the WG the most problem in a way.
With his intelligence and his ability to turn invisible he can do missions with Robin and Brook that Luffy, Zoro, Jinbei or Franky can't.
Like Mr 2, Lafitte, Devon or Morley he can truly cause problems for the WG but it isn't necessarily by combat.