NGE Kaworu was by no means helping Shinji. He deceived Shinji by hiding the fact that he's an Angel with genocidal intentions for humanity sent by the enemy, betrays his trust by going through with that plan, and then forces Shinji into a situation where he will have to kill Kaworu and break himself in the process or give up and die. He was committed to that course of action until he realized Lilith wasn't Adam and he couldn't do what he came to do.

In EoE, Shinji has this conversation with Misato/Rei/Asuka:

Asuks, Rei, Misato: We are nice to you.

Shinji: LIARS! You’re just hiding behind those smiles, but you intentionally keep things ambiguous!

What Shinji fails to see is that this accusation applies to Kaworu, who acted nice to him but hid bad intentions behind a serene smile.

Rebuild Kaworu is more ambiguous. He says he wants to make Shinji happy and perhaps he does, but he's forced to admit that what he offered isn't what Shinji really wanted after all. I hope he's right and he does come back in the next movie so we can get further clarification on his motives.

What we have to keep in mind is that his meeting with Shinji and everything [that follows] is in in accordance with Seele's plan and the prophecy in the Dead Sea Scrolls, and he is well aware of it this time. The deception comes from Gendo, not Seele.

I can see how he would think the plan might bring happiness to Shinji and the Lilin. Casting off the bonds of mortality, having their souls complemented and evolving into eternal beings gifted with the Fruit of Life? That's quite a deal.