To me, it seemed more like Kyube was offering the only solution he knew. Granted, it would result in her becoming an MG which he seems programmed to create; but he also told Madoka earlier that she should wait on that because Sayaka would strongly object to it.
It's more like, "Here's one option, the only thing I can think of. But it's up to you, and here are some reasons why you might not want to. Weigh everything carefully, before making such a life-altering decision."
It is interesting that he said he can't stop them. Even if he wanted to, he couldn't do anything about it. All he can do is create MG's; that's it. Given how Homura beat him up, he can't even really defend himself.
Still nothing said as to what forces an MG to keep fighting, either, even though Homura believed that's how it goes. The series keeps trying to tell us this, but not show why.
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