The way I read it: after she walked in there and "embraced" the idea, she turned the tables on him and tried to make him seem to be the xenophobe while she was the worldly chameleon. Plus, it's a testament as to how little she knows the people who call her "friend". She is so determined to be superior to everyone around her that she attributes qualities to people she supposedly knows that only a complete stranger would consider. Perrin's physical appearance would cause strangers to be wary, and many would think exactly what Egwene said. She should know better, but the only time she would actually consider that point of view is when she has the upper hand over him and is certain he won't pose a challenge to her authority.

She is a good politician...but, in my opinion, good politicians are pieces of crap who are too manipulative to be trusted, will stab you in the back, and are incapable of being friends to anyone. Her actions and behavior with her comrades prove that point.

This just goes to show what a hypocrite she is, not that we needed any more proof. There is so much of it scattered throughout the series that you can't miss it unless you're as deluded as Egwene. When she actually notes the similarities between her actions and someone she condemns for similar actions, you'll notice she excuses herself with some lame reason ("well, the difference between other Aes Sedai wanting to control Rand and me wanting to do it is that I am right!" ).