I can't imagine the Empire - which knew from a Primal in the first place because they'd encountered them before - would mistake Midgardsormr for a Primal. More damning is the fact that there were clearly two separate events - one 15 years ago when the Empire encountered an unexpected Primal, and then another 10 years ago at Silvertear Lake, and I don't think Midgardsormr would have taken off from guard duty to go and put the fear of huge-ass dragon into the Empire at Ala Mhigo! (It -would- explain why the Empire attacked Mor Dhona when they resumed the assault 5 years later rather than move directly south to Gridania, but perhaps - just as a counter-theory - they wanted to beeline for Eorzea's rich ceruleum reserves in Thanalan, and not have to deal with the very protracted siege of the Black Shroud until later? They also could have been after some sort of MacGuffin in Mor Dhona itself all along that they knew about and your average Lalafell on the street didn't, as well. I do truly expect this to be a plot point in ARR; it's the sort of discrepancy this writing team loves creating and then explaining later on.)

We definitely don't have enough information to make any reasonable guesses as to the identity of the mystery Primal, but I think it's fairly unambiguous that it wasn't Midgardsormr and our collective theory that it was was reasonable when the discrepancy in the timeline was less obvious and when we didn't know Midgardsormr was not in fact a Primal, and is shot to pieces like a dead dragon wrapped around a fallen airship now. ;_;