I don’t think so. Not at all. I think that Kyle respects Cartman.

He respects Cartman’s capabilities. And he knows that Cartman is incredibly valuable to the group.

Kyle has come to a point of understanding; that Cartman enjoys hanging out with his friends. And he knows that Cartman prioritizes the atmosphere of the group. It’s usually what has Cartman’s attention. He knows from experience that if something is beneficial to the group as a whole, Cartman will usually go along with it.

Cartman is incredibly competent. And if Kyle gets him on the same page, he can utilize Cartman’s immense drive and competence for his own gain.

And in the later seasons especially, Kyle has reached an equilibrium with Cartman. He knows Cartman well enough to the point where he won’t push him too far, just enough to have interesting banter with him. He also happens to find him enjoyable when they’re in a group setting.

So yeah, Kyle’s morals are completely different from Cartman, but at the point we are now, he’s found some useful loopholes. 

To Kyle, Cartman is essentially a torch. It has a massive ball of fire at the end of it that can burn down the whole town, but as long as you don’t drop it, it works in your favor.