Arlong, upon seeing Zoro's injuries and realizing he was battling in that condition all the time, perceived him as a threat and thought it was better to finish him there once and for all, which implies Zoro's at least in a similar plateau to him. Zoro fought rather evenly with Luffy in Whiskey Peak, with Luffy apparently taking Zoro even more serious than Arlong (with the latter he was still making fun of the situation and fighting in a comical way, although that might not be too telling since he kinda acted the same in the 2nd round against Crocodile), but it's possible Zoro had received an increase in power after recovering from his injuries, so that might not be in itself a decisive factor for Zoro winning. It's tough to say, but based on Sanji being rather surprised at Arlong's strength and being injured badly with an attack from him (sure, Sanji was injured, but not nearly as much as Zoro) and stating his level is totally different from the other fishmen, I'd have to say Arlong is still slightly above Zoro, as I belive Sanji is at least decently close to Zoro throughout the pre TS. Zoro would give him a lot of resistance based on his will power and overall resistence, plus probably negating Arlong's Tokitobashi with his swords technique, but I'd still see Arlong coming out on top, even moreso if the battle is located near water, to which he can use it in his favor like he did against Luffy.
But that's a hypotyetical scenario in which Zoro hadn't been that injured. If it were a Zoro 'post recovery', I'd gotta side with Zoro, as him recovering from his injuries gave him apparently a boost high enough for him to fight pretty well against an angry Luffy, whereas Luffy when angry against Arlong could hold his Tokitobashi in a way he couldn't even move.