I know this is years late, but I had the same issue and unfortunately the only fix I could find was a work around I developed myself.

Here is the same thing I posted on Steam:

"Okay so my work around works good enough:
Download this program:
https://www.highrez.co.uk/downloads/XMouseButtonControl.htm

Then run the program, click the "ADD" button to make a new profile and select the painkiller.exe so it only uses that profile while the game is running.

For the right and left mouse buttons select the "simulated keys" options and the "during" option and then select 2 keyboard keys you wish to use. I used J and K.

UNSELECT the "block original mouse input" checkbox as you still need the original left/right mouse clicks for the main menu itself.

Screenshots of the program and settings located here:
https://imgur.com/a/IAA25VV

Then in the painkiller controls section change fire and alt fire to those keyboard keys respectively.
Play the game!

When you need to do something in the main menu you need to alt-tab out and back in, and then the mouse will work in the menu so you can save your game, quit, etc.

You will of course need to launch the X-Mouse Buttons app and ensure it is running before starting playing Painkiller."