It's never mentioned (e.g. by the Amayar Guide Timna in WH, ch.35, who - on the contrary - indicates that the Sea Folk is still in charge) that there are Seanchan on Tremalking. Maybe you confuse it with Cantorin. Besides that, Alviarin notes that "it was obvious that Mesaana did not know for sure", if the other DF she met, serve another Chosen. And that "she would just have to be careful not to let slip anything that suggested that she had actually visited the site [of the Cleansing].

According to the Wheel of Time-chronolgy Alviarin left the WT to fulfill Mesaana's orders on day 701. The Cleansing happens on day 716. Alviarin returns to the WT on day 723. Thus, it seems clear that Mesaana's orders had nothing to do with the Cleansing. We don't even know, if Mesaana learned about Rand's plan to use the Choedan Kal, since she missed the Forsaken meeting in WH on day 696, where Moridin told the others about it.