Had no idea it used inverted mouse movement when I picked it up from the sale, and unfortunately I never mastered the skill to play games with this :(

Would appreciate any help

As far as I am aware, there is no way to change the control scheme. The keyboard controls are far more manageable, though somewhat slower.

I'm not sure what you mean, but in my game the silencer turns right when I move my mouse to the right and vice versa.

I think that is his problem. In most similar games, the controls are player-centric (like twin stick controls) if you move the mouse to the right, the Silencer will face the right side of the screen, instead of turning clockwise.
In crusader, the controls are oriented on the direction the Silencer is facing, which feels quite awkward from an isometric perspective. I think that's what he means with 'inverted'.