You should go through the entire scene of Nynaeve's debriefing again. She revealed what happened at Natrin's Barrow (Rand's craziest act. If she didn't hold that back, I doubt she held anything else). Siuan was reassured that Nynaeve felt Rand had changed from that point. Egwene herself said that that not only had Rand changed from his insane self, he had a presence that was enough to dominate.

If, after that, Brandon pulls the stunt of Egwene thinking Rand was mad (barring any more insane moves from Rand, of course), it would be piss poor writing. All of Egwene's thoughts about Rand have indicated that she is aware of Rand's great change, but is frustrated with his plans for the Seals. There is no basis at all for her thinking he's mad, as of now. And I doubt she'd make such a charge when Nynaeve will immediately remind her that Rand has a shield of Light protecting him from the DO's taint.

What may happen is that Egwene may notice Rand's link to Moridin in the dreamspace, or notice Cyndane in his Dreams. Egwene breaking into Rand's dreams is a Chekov's Gun that I'm sure will see use in aMoL. IF this were the case, her opposition to Rand's plan may become more entrenched, but I still don't see why she would think he's mad.