Userpoints Karma - Is it possible to only charge user points for down votes?
Adding a module to override User Karma's settings is certainly one option.

Another possibility is to use Rules and Voting_Rules to control your own settings for adding and subtracting user points.

Once enabled you go to /admin/config/workflow/rules and "Add New Rule".  Set it up to React on Event "User votes on a Node".

Add the condition "Check the value of the vote" and if less than 0 add an Action to "Grant points to a user" but make them negative points.

Here's a screenshot of this Rule:


Optionally, if you want to use User Karma in conjunction, you could instead React on the Event of "User was Awarded Points" and test for Conditions and override where appropriate.