How can the energy be conserved, as negative work done on a moving body also wastes energy stored in my muscle? Suppose a particle like object is moving on a frictionless surface. If I push it back to reduce its kinetic energy, it also wastes energy stored in my body. 
Is energy really conserved here?  
Again, if I do not push, but try to balance the kinetic energy acquired from the body, where does my kinetic energy go? I mean, in which form of energy does it convert?
 A: All energy is conserved, but it is not all converted to kinetic energy. Some of the kinetic energy is conserved, some is converted to heat energy. If you apply a force to a moving object, it will apply an equal but opposite force on you. If you were on the same frictionless surface as the object you pushed on, then you would move in the opposite direction you pushed. Some of it's kinetic energy would transfer to you, some would be lost as heat produced from slight deformations (bending or flexing on the object and your hand) from the normal force. If you were on solid enough ground, so it did not move you, and you were able to "catch" the object and stop it, then initially it would move your hand some till your force stopped it. Eventually, the kinetic energy that you and the object lost, would have been converted to  heat or other energy, no energy would be destroyed.
A: Let's assume you are on a surface with friction adjacent to the frictionless surface of the on coming object. The object makes contact with you and you exert a force opposite to the direction of the moving object in order to bring it to a stop. According to the work energy theorem the net work done on an object equals its change in kinetic energy. Or, in this case since the change in kinetic energy is negative
$$F_{ave}d=-\frac{mv^2}{2}$$
Where $F_{ave}$ is the average force you apply, $d$ is the stopping distance and $v$ is the velocity of the object on contact. The assumption here is that the maximum value of the force you apply does not exceed the maximum static friction force between your feet and the ground, so that you do not slip and accelerate.
The fact that you did negative work means that you removed energy from the object and absorbed it into your body. Regardless of the exact mechanisms involved in absorbing the energy, it results in an increase in the internal (microscopic kinetic and potential) energy of your body. Thus, energy is thermodynamically conserved. 
However, as a result of absorbing the energy of the impact, as well as converting additional chemical potential energy to fuel your muscles to absorb the impact, the rate at which energy is normally transferred out of your body when it is in equilibrium with its surroundings, may increase in the form of heat conduction, radiation, and convection through perspiration and more rapid breathing, all of which reduces your internal energy until your body is once again in equilibrium with its surroundings. 
Hope this helps.
