I was a little (okay, no, a lot) confused at first as to why he went straight from telling Cloud that he had no interest in doing anything to Zidane to "setting him up" -- but then I figured out that Kuja was either really trying to help beat Chaos or just doing the same thing that Kain was.
Let me explain.
As you mentioned, he informs Zidane that beating Chaos would cause all of his servants to fall too. He also tells Zidane that this works both ways for Cosmos's team.
So, right here, Kuja has just given "the enemy" valuable information that he didn't have to share in order to get Zidane to trust him. Zidane already trusted him.
Despite Kuja attacking the warriors of Cosmos when the Emperor, Kefka and Ultimecia show up, I don't believe he was doing anything more than trying to protect them from being killed by the manikins.
Notice that with the villains on the scene, Kuja even tells Zidane to run: "Zidane, take your companions and go--." He does so again when he fights Zidane: "You should probably run--before you no longer can."
Now ignore the tone with which Kuja says that last one to Zidane and just look at what he's actually doing. He told his supposed enemy to run away twice after -- if this whole thing really were a trap to kill that enemy -- the "plan" had worked? It doesn't make sense.
Notice as well that Kuja tells Kefka to put the manikins away and says he'll do the fighting himself. Fighting which he wins -- and yet he still "fails" to kill not even one of the three warriors he'd just defeated before they escape?
It becomes pretty clear, I think, that Kuja didn't want Zidane and his companions to be defeated by manikins in this scene, so he decided to play the role of the treacherous schemer who lured them into a trap.
I think this comment to Kefka after the fighting cements that Kuja really did let them escape deliberately: "You think I let them slip through my fingers?"
Notice, as well, how depressed Kuja looks and sounds after the battle. In order to save Zidane and the others in that scene, he had to lose their trust.
The only question that really lingers is what was Kuja's original intention? Was he really trying to help them find a path straight to Chaos, or was his actual plan tied to what he told Cloud at the beginning of Report 1 -- when he asked him if he shouldn't kill Tifa in order to prevent another villain from doing it?
I think Kuja intended to either help defeat Chaos, or he was planning to lure Zidane and as many of the other warriors of Cosmos as he could into a trip to kill them himself so that the manikins couldn't. The fact that he didn't kill them after beating them in that scene, though, suggests that it was a genuine attempt to help defeat Chaos.
Anyway, when he realized his plan was blown, he took measures to protect his place in Chaos's ranks so that he could try again in the next cycle -- but, of course, his plan failed because Kefka set Kuja up for a fight he would lose, so that he would be dead at the end of the current cycle when Shinryu reset things. Apparently, Kefka could knew he could manipulate Kuja's memories when he showed up in the next cycle, and that's why we're stuck with a Kuja who's just a little bitch that hates Zidane in the first Dissidia/cycle 013.
