But he already suspects Harry was present: he thinks either Harry or Draco confronted Barty, and that one's presence necessitated the other's (even though that wouldn't have been true pre-Toadifying).

Fawcett is the logical leap because it can happen even if he can't confirm either Harry's or Draco's presence: two kids really thoroughly disappeared, even though they themselves didn't have the resources to make it happen, in a circumstance where adults either dudn't assist or assisted so secretively that no one detected them. A kid really thoroughly disappeared from Hogwarts, and the "signs of struggle" didn't involve any human blood... ergo, maybe they disappeared her too.