You would like to think that the mouse would not be so scrutinous as to deny a child boarding in this scenario but after readin some of these replies, I am outraged as to what lengths a CM could go.
I would say to make sure that your hcild is wearing shoes that have the thickest sole. Stand upright and take a breath.
You're OUTRAGED? That's a little over the top don't you think, especially since the CM can make the child take off their shoes. Seen it.
Does the phrase CYA ring a bell? In today's world, that is the most important advice you can give or get. People sue for everything and don't take their own liability into account. CM's are doing their job.
So, here's a scenario . . .
Little Johhny is 39 inches in his bare feet. His parents get him in his thickest soled shoes, and get him to stretch big and tall. He gets to the line and he's really close.
Now, you're the CM doing the measuring. . .
Regardless of what happens, you are putting yourself in the firing line. If you say "I'm sorry, he is going to need to take off his shoes" you stand the chance of getting a complaint against you, and your boss comes down on you. Plus you're going to have Mrs Johhnysmom yell at you for who knows how long about how you are ruining the entire vacation, and Johhny should be allowed to do anything Johhny wants to do, plus there is some wiggle room built into these safety measures, and it's only a little bit, why can't you just turn your head.
So, as the CM, you turn your head to avoid any confrontations.
Bird crap flies into Johhny's eye. Now Mrs Johhnysmom is screaming at your boss because her precious Johhny should never have been allowed on the ride in the first place because he wasn't tall enough, and you as the CM should have been more proactive.
In today's litigious society, people are irrational, self-centered, and entitled to what they want, to hell with the rules.
A CM that is doing his or her job properly, and enforcing the letter of the rules isn't doing any activity that should bring a sense of outrage. I for one wish that all CM's would take the approach that the rules are the rules. Maybe then we wouldn't have to endure five thousand threads like this one, or the heely threads, or the line breaking threads, or the pool hopping threads. . .The CM's aren't inducing the outrage, it's the guest's actions and attitudes that get me hot.
Try riding those biggies first thing just in case! Good luck! 
I will say that I was pretty surprised the next day at MGM when he breezed right through the RnR line 4 times without being stopped and measured even once (also a 48" requirement). Given that RnR actually goes upside down, I'd think they'd be more careful in checking to be sure no one is too small for the ride restraint to work properly. 
