Smoker said that he has to achieve a higher rank in the marine to be able to do what he wants more freely.
By now he cares for his position(until he reaches a rank he thinks is enough to hunt down his goals), he does what is necessary so long.(Like hunting down low level pirates, which is more boring for him than anything else.)
http://read.mangashare.com/One-Piece/chapter-439/page015.html
Luffy gave Smoker a goal in his life, he now wants to achieve "Stopping that strawhat-bastard" which Smoker missed before in his life as a marine.
He isnt interested in fame or high ranks, he is a guy who wants to be a marine to help people. That he was able to do even as "just" a capt
n.
He already saw that the world isn`t just that "black or white" the WG wants to make you see the world.
So just moving like he is ordered was never his intention..he always tried to be differnet and thats also the reason why he got trouble with the officials..which resulted in his low rank, even when we know how strong he is(and also being a logia-user).