What the Fark is nothing but an intelligent almost homonym of What the Fu*k, which is made up of half English and half Hindi, using the word 'fark' which means 'difference'.
The literal meaning of the phrase What the Fark would be 'What's the difference' and hence has nothing to do with foul language so to speak. The makers of the song have also written the word in many places in the video and have the 'r' pronounced quite clearly, probably to get it passed easily from the censor board, though end of the day this WTF is going to remind people of the regular WTF only.