How does the power station compensates for the current that flows down to earth due to domestic body-current faults?
I know current flows in a loop and energy is used to move it in a loop. Now suppose we get a single phase AC (220/120V) electricity supply for our home and we have earth connection to prevent shocks from the current that leaks on to the metal body of our appliances.


OK so far.


  So we have a circuit loop in which current (electron present in the wire) flows from station to house and back to the station (the direction of electron is opposite to that of conventional current flow). Also there are fixed number of free electrons present in this circuit loop.


Stop thinking about electrons. It doesn't help. Just think of voltage, current and energy flow.


  Now consider a situation where somehow current leaks to the body of a appliance and goes to ground instead of returning back to the power station( due to earthing). 
  How is this lost current compensated by the power station which never receives it back ?


The neutral conductor is "neutralised" by connecting it to ground. If there is no ground reference then there is no reason for the current to flow to ground.


  I was talking about conventional current so if you talk about electrons I can reframe the question as how does the power station deal with the extra electrons that flows from ground(earth) back to the loop?


Again, thinking in terms of electrons is no help. Current returns to the power station through the ground and back to the source - the generator or its transformer in this case.

Further reading:


Does electricity always flow in a closed loop and why does current flow to ground?.
Why is neutral wire connected to ground at the transformer?.