The 28-year-old was penalised during his side's 35-11 win over the St Louis Rams on an unnecessary roughness call for hitting defenceless receiver Chris Givens as he attempted to catch a pass from Sam Bradford in the endzone.
"I think I'm just supposed to let them catch a touchdown now," Whitner said on SiriusXM NFL Radio.
"I think that's what the National Football League wants, but I'm not going to give them that.
"I'm going to continue to play physical, continue to hit the right way, lead with my shoulder, and I'm not targeting anybody's head."
The 49ers are 2-2 after week four of their season.