Don't penalize QBs for a kneel-down.
If your QB has done well enough during the game he doesn't even need to try on the last drive, you shouldn't end up being penalized for that. Sacks don't count as negative run yards, why should kneel-downs?
We had a team in our league this year literally lose by 0.01 points because his QB knelt on the last play of the game. It's ridiculous.
Rick Blair commented
or change to .1 per rush, that would even out the kneels with minimum impact on real rushing attempts.
Just change your league's settings to give 1/2 point for each rush attempt. Then your QB will show a small increase for each kneel down.