I agree - no doubt I'm an overprotective mom to some.....on one trip when a friendly stranger gave us one FP for TSM - DD wanted to ride - she was 12 but I didn't want her to have to wait in line alone. She's a smart child who would have been fine in terms of behaving and Disney always feels like a safe place but I wasn't comfortable with her waiting alone. The CMs at the FP line understood completely - I told them point blank I knew I couldn't ride (only had one FP) but I wanted to wait with her - they let me
OP I would ask at Guest Relations if there is any way for you and the smaller child to wait with the bigger ones. I don't know - never been in that situation but I don't think it would hurt to ask.
I would also ask the people letting you into the line - although I suspect they've probably seen a lot of parents trying to 'pull a fast one' and 'slip' a smaller child onto a ride (which I know you're not trying to do - just saying they may be somewhat jaded) if you could stand in the line. Generally (I believe) there's a 2nd measuring spot just before the actual ride you could leave the line at that point easily having waited for most of the line. I know at Kali River Rapids when you get to the 2nd measuring spot you can see the actual ride vehicles so you could leave the line (with the shorter child) and feel good that the other 2 were going to be OK with the short distance they still have to go (in fact at Kali if it's not too busy you could stand just off to the side and see them load)