Is there any hook to multiple total price only in payment method
Personally I would rather use hook_commerce_price_field_formatter_prepare_view.


  This hook is used by modules like the Product Pricing module that implement ways to alter prices prior to display. 


That way you could keep your prices as regular dollars internally, and only display them as kilodollars for your customers. Regular storage will make it easier to interact with gateways.

Other way, although I'm not sure about it's specific implementation, would be to define second currency. You can have a shop that sells in Euro and USD, and internally re-calculates prices to meet client's payment method, right? Maybe you could define kilodollars just he same way, with exchange ratio 1000:1 to regular dollars?