jpod, i'm not quite sure what you are saying in your post. I believe you agree with the grossing up of the fee but are just handling it differently.
Instead of taking out the distribution amount of $872 and the fee of $125 as a single transaction, you are saying that it would be better to split them up. Am I interpreting this correctly? If you are in control of the preparation of the 1099-R, then it shouldn't matter if you do this separately or as one transaction. You would end up putting $872 as the taxable amount either way
I agree that the $125 fee sounds steep.