u said u work in a diff state other than the one where your employer is based at. legally if thats the case, ur employer should get the approval from state A (where u work) and only then you can avoid state B's state tax. usually i noticed that the desi employers don't get this permission to work in other states. when they file for H1, they get an aprroval to work in the current state (where they are located). if in a case when we have to work in other states ,legally they should get the approval, which they don't.
what you can do is ask ur employer to get the approval of state A else you have to forget the state tax u r paying now.