There are already Seanchan in the WT, namely the damane who were captured during the raid. But we know from Egwene's Dreams that one Seanchan woman in particular is apparently linked in some important way to her future.

However, I agree that Mesaana might also very well be the danger which threatens to kill Egwene, if someone won't save her in time. Maybe Rand or someone else capable to save Egwene will learn about Mesaana being in the WT from Verin's letters (e.g. Mat with his medallion? could be his crucial decision to either save Moiraine or Egwene).