We just came back last night from the UK. My husband and I went through the non-EU queue together and explained to them what was up. The immigration officer obviously had no idea what he was supposed to do in a case like this. He kept flipping through my passport, and I said, If you're looking for an up-to-date stamp, there isn't one. The GNIB wouldn't give me one. He asked me why not, but I told him the people at Burgh Quay just said there wasn't anything they could do until the Justice Dept. processes my application.
Supposedly, the Burgh Quay people had put a note in my file about it, but whether that was available to the immigration officer, I don't know. We showed them our marriage certificate; we showed them the confirmation receipt we got from the Justice Dept (that little piece of the application that they sent back with a date stamp). They asked us other questions like where we lived, and whether I'd ever had any trouble entering Ireland before.
They let us through, and the guys were quite nice. I think they believed us, basically (if not, we had just been to the UK for a reception with his family, so we'd have been able to show them all the cards and gifts we'd received!) but didn't know what the procedure was for a situation like this. The officer gave me another 1-month stamp and, when I asked, said that yes, basically I'd have to go through all this again if I leave the country again.
tomasmv, this might be useful for you: my husband asked them what would happen if I had to travel alone without him, and the officer said that, as long as I had the marriage certificate, that said my husband is an EU citizen, it should be okay.
But basically, it is all up to whether or not the immigration officer at the airport believes you.