...that Tuon was going to appear in the streets with several damane while Rand was incognito, therefore forcing him to keep hide by 'kneeling to the Empress'. Didn't happen though!

As far as the Seanchan go, Tuon is completely crazy. She seems forced by duty and honour, but she knows that the Dragon and his allies are very dangerous to her and her territories.

Nevertheless, it does appear to have been a knee-jerk reaction to Rand. This could either be ta'veren effect acting in such a way that the results are very indirect but beneficial to the Pattern, or Rand's new darkness corrupting the Pattern more than aiding it.