Rand's children won't hardly have any big role in the story!

Elayne has months of pregnancy to go still. They'll show up far into the LB or in the epilogue part only. They would be named Rand and Elayne, or Rand and Egwene and it still would create zero confusion.

Jordan wasn't really afraid of confusion anyway. Contrary to popular belief, he's had several characters with the same name (even within the Two Rivers itself.. a few Hus for instance) or with local variations in which only spellings differed. Worse, most of these people were fairly minor players much harder to keep track of (including two historical Queens of Andor)

He put enough of those to tone down the weird effect having everyone get a unique first name would have created.

Not that I really have an opinion on the children's names... but I don't think "confusion" is a good argument against giving them names of other characters.