Anyway she could not guarantee us that we would have a seat in the dining room....
This is the line that jumped out at me, and I agree with the others that you should try a different TA next time. There is no way this statement can be true. Also, I don't understand how there can be a cancellation penalty from HAL if final payment is yet to be due? The penalty she spoke of was likely from her agency, but not from HAL. And, it would have been a real pity had you cancelled based on the misinformation she provided about the dinner seatings.
I'm glad you came here to get the real scoop, yet this "TA" needs to learn a thing or two. I know this is the first time you used her, but I wouldn't return. You might want to consider dealing with her supervisor for your subsequent calls on this booking.