Oh,dear, I don't know where to start. I'm looking at this as both a parent AND an educator so please bear with me (especially as I'm on the iPad so I may not catch all of my typos). First, taking the lunch away was not an appropriate way to handle the issue, neither was charging your account ( and an administrator should get the cafeteria to fix it). A better way to handle it would have been for the aide to share the concern with the teacher who would then call home to discuss it. It is your choice whether you wish to choose this battle to fight (getting that money back).
This year new and more stringent laws go into effect concerning what may be served for meals in schools. This information should be available on the school system website. If not, let me know and I will dig up a link for you.
My school is a Bronze School in the Healthy Schools program. We must do several things to contribute to the health of our students & staff ( and I've talked about them in other threads). We have a school-wide "healthy school food policy" that we send home on the first day of school. It covers what is okay for class parties and a reminder to please not send family size bags of chips and soda to school as a lunch plus a few other details. For the most part our families are very supportive of these efforts.
I understand about picky eaters. My youngest has tons of food allergies, is picky & wouldn't eat any bread. Packing a lunch for him on days he couldn't buy due to allergies was very challenging. I know this folks wondered why he never had a "sandwich" & instead had only the meat. At least he would eat apples, cucumbers & yes, goldfish!!!
If I were you, I would just chalk this up to first week craziness since you've already contacted the school, and just be on the alert for any further issues. If there are any further issues, start with his teacher first ( conference) and then go to the Principal. The teacher MAY be able to help but really has no control over the cafeteria. the Principal would have some say but if it involves policy from the district, state & Feds, you may need to go higher. Choose your battles.
Had I been on lunch duty with your baby, I would have wondered, but figured he was a picky eater & made a mental note to keep an eye on him to see how much he ate. If he ate it all & still seemed hungry, I'd have called home to let you know so we could figure out what was best for your little guy. Kindergartners are notoriously picky eaters so chances are good you'd probably never have heard from me about this because he would have eaten what you packed & been fine!
I would also recommend being sure to go to back to school night if only to get information about the day's schedule and any info about snacks provided for the kids.
Hope that he has a wonderful, fun year!