It's not so much that. I just bought a 3rd party memory card from a local pawn shop for $5 and I can transfer saves to and from it (my only GC title also has protected saves.. go figure). It's just getting the game to recognize the save as not corrupted. I can't even do that with two memory card files on the emulator. AFAIK I'm going to need either a memory card or know how to edit the save to work with my memory card.
There is an app that can make a 3rd party memory card work as an AR but that stopped working with system menu 3.2... My Wii came with 4.1. I hear it's very risky downgrading the system menu, especially w/o a vulnerable boot2.