Sapiens seemed very pseudo-scientific to me. It seemed like Hariri had one agenda and was trying to push that desperately.
I think you may be confusing "agenda" with "perspective". He was pushing one perspective: his own, as all authors do. But it's our job as readers to understand the author's perspective and recognize it as such.
Neither history nor anthropology permits storytelling without a perspective. There's always a perspective. Reading for learning means understanding that perspective and determining which aspects (if any) we'll choose to adopt ourselves.
If you're used to science, it can come as a surprise that a person can willfully ignore (not just focus away from, ignore), all but one option for an entire book, and it still be considered an intellectual effort as opposed to a sales pitch or campaign tool.
Of course, sometimes none of the theories can be proven or disproved. So unless you want to leave a black hole you simply choose the theory that fits best, with the risk of it being overturned in the future.