3% is 3%. It's nonzero, so that's unfortunate. It's not a large fraction, so it's just not a time sensitive problem.

Is it worth tying up media, political and financial resources in blaming+lawsuits over the optics of a 3% fee, instead of just waiting to deal with it next year?

Your question implies that 3% of loan applicants get nothing because of this fee (which is inaccurate, since congress will just authorize more loans as long as it's politically convenient). As I said, it's unfortunate, but it's not world ending.