They were irritated by all his tempter tantrums and freakouts, plus from what I hear they liked Herzog and felt that Kinski's behavior was an insult to him.
I find it completely awesome that Herzog mostly declined because he wanted to finish his movie.
Wow. He makes it sound like he was 50/50 on the decision. I imagine if the tribesmen had killed Kinski he probably would have used it in the film somehow so his death wouldn't be in vain.