Drupal 7 Commerce - How would you increase or decrease a checkout total price depending on payment type?
In the checkout methods rules you should be able to add an action that decreases the total or subtotal cost.  So when a certain payment method is used, the subtotal will decrease.

If one of those rules actions isn't available you might need to look at some other modules like Commerce Rules Extra.

Another option would be to apply coupons automatically to orders with those selected payment methods with the Commerce Coupon and Commerce Coupon Fixed Amount modules.  That might give you better control over how many times a user or how many users can use a discount like this.