LOL, we've seen recently. Not that recent but recently some of Doflamingo's power ( He smashed smoker with little ease) . Just how bad do you think doflamingo could've messed up Crocodile during the great war?
Thats true, if he was serious about ending Crocodile he could of killed him with Haki when he took his head off, but then someone of his skill set I would imagine he had Haki at that point.We don't know if Doflamingo could hurt Logias before the timeskip,so we can't really say.
Not to mention, Croc prob. didnt have haki at the time and I'm 100% sure he has haki now since he went to the new world.I think at the time of the war Crocodile was stronger then Smoker.
Smoker only is assumed stronger for a couple of reasons:
1) He has his Jutte which can hurt DF users
2) around the same arc Croc was defeated by Luffy, Luffy couldn't handle Smoker at all.
We tend to forget that Croc killed Luffy on 3 occasions but was saved 3 times too.
Luffy only beat Croc because of his weakness.
Smoker was just a mere commodore at the time, look at all the marines who are stronger then him (Captains, vice admirals and admirals)