On the issue of what Wesley thought Kirk was trying to prove, the obvious scenario would have Kirk delaying aborting the simulation because he wanted to show Wesley that M-5 was a deadly mistake. That's a plausible and somewhat defensible action up to the point where M-5 began doing real damage and killing dozens.
Wesley's comments would actually make sense in the context. His first objection still involves the understandable initial horrid belief that Kirk wants to prove something, even though the likelihood of that is rapidly diminishing already. In the following ones, Wesley is disabused of that idea and simply pleads Kirk to abort M-5's attack by any means.