First, let me just say that those moments during the liberation (the assault on the two schools and such) always wierded me out because I was always imagining modern-looking schools, teachers and students, even though the book never directly describes them as such. Of course some people might say that it was Lewis' way of having the old and mythical triumph over the new and pragmatic (which is probably more truly said of the Silver Chair). I had a hard time deciding the first time I read it just how medieval-ish the Telmarines really were.
About the pigs- I don't know why this would really bother anyone that much, even if it was true. Lewis was probably using these boys and their school to represent what the prevailing values were that Telmarine youth were being taught- hence the disagreeable nature of their country. (It could also possibly be inspired by George MacDonald's The Princess and Curdie, which features certain ill-mannered people slowly becoming animals and monsters which share the character traits they had displayed).
But like you said, the whole thing is somewhat uncertain, so there's no need for anyone to take offense at it, even if you are bothered by people being turned into pigs at tender ages. It would be a scene probably best left out of any adaptation, though, if it really has that much of a problem just on paper.

I tend to agree that the book is deliberately vague about whether or not it's true, and very likely for the exact reasons that you said. One thing when it comes to whether or not I believe it, though, is that Rabadash experienced a similar punishment as a grown man after committing an act of treachery worthy of death. Despite this, he was given an opportunity to be turned back to a human and even lived out his days still ruling Calormen (though of course with the fear of turning back if he ever left Tashbaan).

Granted, this story was written well before that and from a "meta" perspective, perhaps it's not fair to judge the intent of this book by what came later. But within the stories, it doesn't make a lot of sense to me that these children would be punished so much more severely than a grown man with no hope of mercy. (Besides, it's always bothered me, the thought that one of their parents might ignorantly catch one of these pigs and make a meal of it - *shudder*!) I prefer to think that the boys were just scared senseless, and a legend grew up after the fact.