How can we obtain frequency difference of two waveforms?
The input to the VCO of a PLL will be related to the frequency of the input when the loop is locked. 

For example, the LM565 has a typical VCO sensitivity of 6600Hz/volt when the center frequency is set at 10kHz, so the VCO control input will change by about 150mV/Hz when the loop is locked.

If you have two waveforms you could use two PLLs and subtract the VCO input differences- you'd also have to remove some offset voltage and calibrate the gains, no doubt.