You will not be able to determine how much interest has been earnt during your time in a non-compliant superfund. It is just not the interest that is not sharia-compliant but there are also other asset classes that can be non-compliant. Which then makes it extremely difficult to determine the amount that you should omit from the fund.
Even if you were to determine you cannot remove this from your Super due to the regulations. You may just want to provide a certain amount to charity when you can access your Superfund in retirement, to ease your conscious.
Due to your good intentions may Allah excuse and reward you for this thought. You do not have to worry too much about what has happened prior to you not knowing there were Islamic alternatives for Super. Now that you know, it is your duty to ensure your retirement fund is Sharia Compliant.