I don't think Weaver really understands the nuances of morality and religion and so forth well enough to be able to discern that what Ellison was teaching was overly simplistic and silly. It all probably seems very illogical an inefficient to her anyway so she probably just just thought that this sort of thing worked for humans, and it clearly seems to work for Ellison, so maybe he can teach it to a young, impressionable John Henry.

He also had the advantage that he already knew about machines from the future so he's mentally prepared for this concept and it wouldn't shock him or completely freak him out. And she knew he would likely keep his mouth shut since he didn't spill the beans about Cromartie even after the massacre.

Of course we knew she had a backup plan to, ahem, 'relocate' Mr. Ellison in case his tutalage was not working for John Henry.