Emperor Joker was a one off story character so shouldn't even be a factor in this. Pretty much every major character in DC has obtained omnipotence once in their lives just for some story line but it only happens once.
Joker Venom wouldn't work on Sasori, Pein, possibly Kakazu and Hidan. I say Pein because he uses retainers to fight which are zombies. Also Joker Venom would only really work in small spaces where it could be set as a trap and everyone in Akatsuki has reactions that would let them avoid it. I doubt Joker could gas out the whole city without it being painfully obvious i.e. putting the venom in balloons or something. You have to remember, someone like Itachi is a genius who can analyse situations in seconds. I doubt he'd fall for any old trap. Same with a lot of the Akatsuki. Other than Joker Venom, I don't see how he could really kill most of them, especially seeing as they travel in teams covering each others back and can communicate telepathically. If one of them goes down, they'll be able to find out how and be able to prepare a counter.
Like I said before, Akatsuki will have no qualm about destroying everything to get to Joker which is something Batman never does.