He's very curious about the ancient world. After all, he spent decades unraveling Old World knowledge, going so far as to awake the ancient machine that's presumed to be HADES. Then Aloy comes along and expedites not only his journey to learn the truth, but pretty much doing the work for him. He was listening in on Aloy's Focus, he copied Sobeck's notes, he basically points Aloy the way, coaches Aloy to keep going, and so on. He didn't even show himself in physical form until he had to, and even that was sparingly. Who knows what he was doing, where he was. But we had to play along, since he was the only one who knows what he was doing. We didn't have to trust him. And then, when he learned enough, he suddenly departs, leaving Aloy to fight off HADES. No support in the final battle, just waiting to gain remnants of HADES, once the aftermath blew over. Aloy was a little ignorant missing this.
Honestly I think Sylens is still influenced from his time with the Eclipse. Remember when you talked to him before you left GAIA Prime? he said that we would do it again if he could. I'm sure that he knows that HADES is a bad apple and obviously a threat to all life on earth, ever since HADES put a kill order on him. But it's not like if Sylens wanted to rid of HADES completely. Sylens needed to know more about the Old World, his life basically depended on it. His time with Aloy made him learn that there's still more to know from the threat, in spite of the threat being so close to wiping all life. Though I think Sylens knows this much: he probably won't try to resurrect HADES again. But who's to say he will do anything to learn the truth?
Another bit I found odd is the manner which he captured HADES into that lantern. From that alone, Sylens knew that Aloy will be able to kill HADES, but not enough to wipe him out. The Master Override was just that, an override. Didn't mean HADES is dead. Sylens capturing HADES like that was almost black magic, out of all the things we saw thus far in the game. Can't help but think how in the world Sylens did it.