It certainly doesn’t look good for the airline whose flight attendant reacted to a toddler’s saying, “Bye, bye, plane!” by suggesting his mother drug him to keep him quiet. As a parent who has taken a small child like that on a flight, I can attest to the need of the parent to do what it takes to keep the kid from freaking out and screaming on the flight. Having a little boy say “Bye, bye, plane” doesn’t even rise to the level of notice, let alone alarm. And I’m assuming, here, that the flight attendant was asserting some kind of security issue rather than it being a simple matter that she can’t handle kids.
Either way, if the facts come out that the mother did not threaten the flight attendant (as the F/A told the pilot she did) then the flight attendant should get to work dusting off her resume. If I were the airline management, I’d make it loud and clear that she was gone, too.