J.H.
My daughter was 6 weeks old and she had to be put to sleep to have a CT scan of head. She was having, what we thought were, seizures.
I was terrified of her being sedated, but everything was ok. She was drowsy when she woke up, but it was just typical (anyone who was sedated the way she was would have been drowsy.)
If the doctor says this is what needs to happen, then I'm sure your son will be ok. Doctors don't like sedated children if it's not absolutely necessary.
*hugs*