Multiple visa

I understand that if we got a single entry visa we need to get an approval upfront from the employer or else we will have issues with immigration.  How about having multiple entry visa, even then an employer can stop an employee from travelling back to his home country

I'm sorry, but your question is extremely vague and impossible to understand.

Are you talking about single versus multiple entry KITAS visas sponsored by your Indonesian company employer, and in association with a work permit…or what?

Yes, just need to know about kitas having single entry vs multiple entry on work permit.  With multiple entry kitas, does the employer has got any right to stop employee to travel back

With a multiple entry KITAS sponsored by your employer and in conjunction with a work permit, your employer has to approve any exit permits from Indonesia.  And btw, the same goes with a single entry KITAS. 

This is to safe guard employers here from foreign employees "running out" before fulfilling the obligations of their work contract.

Many thanks and really I hope this information will benefit most of the expats