Technically, Egwene was wrong to scold the rebels for splitting - the split was the right and necessary thing to do, and that doesn't just change because the Tower is whole now. The WT AS were wrong in their support of Elaida; misguided and ignorant, true, but still in the wrong.

However, pointing out this fact would achieve nothing. If anything, it would tick off the remaining WT Aes Sedai, and threaten Egwene's grip on authority. What she needed to do was demonstrate that she was impartial to sides - neither the rebels nor loyal Aes Sedai mattered; her loyalty was to the Tower. To achieve that end, it was a wise political move to 'scold' the rebels a bit.

She was effectively reassuring those Aes Sedai who stayed in Tar Valon, that there wasn't going to be a radical change in hierarchy. She was telling them that she could see things from their point of view.

I would liken it to a mother who scold her children when they get in a fight. It doesn't matter who was right or wrong, you shouldn't have been fighting.