well speaking as an entirely unqualified medical non professional who has not taken a complete history or examined you and your lifestyle in any way at all, I'd say yes you'll be fine, or not as the case may be. You will probably make it worse of you try and make the pain go away by driving it from your knees with hammers though.
I know cycling forum, other people ride fixies etc but they're not you and your knees. You could try as tyred said, put a more toothy sprocket on, have a play about with saddle height and angle, make sure your knees are pivoting correctly over the BB and that the cranks are suitable length for your style, don't ingnore the bars either, height and reach could shift your body geometry on the bike and make a difference, but if its worrying you maybe find a physio to have a chat with