No competent writer of utility classes would write something which accepted a FileReader, when accepting a Reader would be much more user-friendly. So in my opinion it should really be changed.
But I'm sure you are right, you won't have the power to get it changed, no matter how badly it was originally written. In the meantime your workaround is to read the data from that InputStream and write it to a file on the local disk. Then get a FileReader from that file once you have finished that step.