How does a wing mounted jet engine on a supersonic airplane prevent the interference in the flow due to Shock?
Flow conditions are not so different, only the reaction of the flow to an obstacle is. By shaping the intake appropriately, supersonic flow is handled easily, and shocks will be helpful in decelerating and compressing the flow.

However, supersonic flow demands sharp intake lips which are hit by the flow at the right angle, otherwise drag rises quickly to intolerable levels. These sharp lips will cause flow separation in subsonic flow when hit by the flow at an angle, so aerodynamic tricks like bypass doors need to be added to the intake to keep flow angles at the intake lips in check.

Note that the intake will ensure a flow speed around Mach 0.5 at the compressor face of the engine, regardless of flight speed. Therefore, the engine will not need to be optimized for supersonic flight. However, to keep its frontal area low and the nozzle speed high, its bypass ratio should be low. The only troubles this causes are increased engine fuel consumption and noise.