No, you are not paying tax on it twice. You only pay the premium once. You either pay it with taxable Social Security income, or you pay it with taxable income from your job. You can do whatever you want with the other taxable income that you don't use to pay the Medicare premium.
If you have the Medicare premium deducted from your Social Security benefit, then you are paying it with your Social Security income. You are not using the extra money from your employer to pay the premium.
