The problem with many of those philosophers/scientists is that they do not believe in free will to begin with. That flawed fundamental assumption leads to flawed conclusions.

Many is not the same as all.  Also, I think you may be mistaking what for some is a conclusion as their premise.  Some likely disagree with your premise as well that god has a plan for mankind requiring agency to work.  That doesn't make them stupid or mean they're lazy thinkers.