I would have been scared to say anything for this reason as well. Which suggests that the only solution is to take a bigger laptop bag that she wouldn't assume would fit under the seat (which is silly of course).

I too have a smaller than the average sized bag but although it actually can fit under the seat in front, which is one reason I got it so that I know I will always be able to fit it in on a flight (no gate checking), it isn't obvious to other people that it can since it does look bigger, so no one tries to take it out of the overhead.