How is this a second in command moment? By protecting the crew in some way? In that case, Sanji is first mate for tricking Mr. Crocodile, protecting the crew, and by creating the whirlpools in Enies Lobby that caused the initial fire in the Buster Call from missing the tower they were on.
Giving orders during the need for navigation makes Zoro second in command? Because I think there's another crewmember that you can find giving even more orders during navigation...
Giving Luffy advice on what it means to be a pirate captain? Robin did the same thing when she warned Luffy that Pirate Alliances often end in betrayal. Sanji also did this when he kicked Luffy, telling him that as captain, he needs to get over himself and can't let his emotions compel him to say anything carelessly.
Funny, because Luffy completely ignored him here and let Brook join anyways, who later went on to save and help them not only in this arc, but also save Nami's life from Sheepshead on Zou. So Brook joining was in their best interests.
Sanji did the same thing on Dressrosa. Both times, Luffy went on to goof off. Convenient you ignore the next page when Luffy uses UFO and Zoro complains that he just told Luffy to stop goofing off and he goofed off anyway.