Again, it does not make Goldanna's quest pointless. The quest is about Alistair finding out what a family really is and if he truly willing to find that, not who is his real family. The results of the quest ether has him see his companions and the wardens as his real family or that he is convince he does not need a family at all. And Loghain and Alistair are just say what they think is true. What they were told. They both don't have first hand knowledge of what happen with Alistair mom. Heck, Alistair may not even know when he was truly born. It easy to switch Alistair for a baby that die, even if the baby die 2 years from his birth.
Loghain had a conversation with Maric who presumably knew a thing or two about the child he helped create. Maric told Loghain that he didn't acknowledge Alistair as his son for fear of turning Rowan into a concubine in the eyes of the people of Ferelden. A woman who is long dead, cannot be a concubine. That dialogue implies that Alistair was born while Rowan still lived, which should rule out Fiona as his mother.
I can understand that people may simply prefer Fiona be Alistair's mother, because they find it more interesting. But to stubbornly refuse to admit that it creates inconsistencies with some of the dialogue in DA:O, is an example of burying your head in the sand. It does require mental gymanstics in order to explain away. You're reduced to finding an out-of-game explanation for the inconsistencies between The Calling, Bioware's Twitter canon, and Loghain's DA:O dialogue, not to mention the Goldanna quest line.
As for Alistair being 'easy' to switch as a baby...I'm not so sure. We're dealing with a quasi-medieval universe where babies aren't born in modern hospitals. They are most likely birthed by midwives at home, surrounded by relatives. For the commoners we aren't talking a large multi-room manse either, but rather a one or two room hovel. In order to pull a baby switcheroo you need a midwife that is in on the plot and able to both sneak in the replacement (Alistair) and sneak out the original baby, potentially past numerous witnesses. And you now either have to do something with the stolen infant or eliminate it. I won't go so far as to say that such a plan would be impossible, particularly in a universe where almost anything can be explained away by 'a wizard did it,' but it does seem to be a bit of a convoluted plot. And why switch babies at all? Why not simply raise Alistair as an orphan found ditched on the side of some road? No complicated plot necessary, and no one would be the wiser.
There is just so much that doesn't make sense at all once you make Fiona the mother, rather than that human serving girl from Denerim.