That freakout, and that worry (which you apparently have since discovered was unfounded, I hope :) is precisely what the meditation helps you deal with, among other things.
And yes, it kind of sucks that the teachers can't speak more at liberty with you. But there's a lesson there too: in the end, the answer to any trouble you might have is to simply find the craving and the aversion. Find the ignorance in your misery. You were safe and taken care of, and you felt you were at risk. You were wrong.
Blaise Pascal famously claimed that all of man's problems stems from the inability to sit quietly in a room, alone. And we are not able to do it, either. Vipassanna is the rather upsetting path toward learning to be able to sit quietly in a room, alone. And it's very simple, but not at all easy.
"Vipassanna is the rather upsetting path toward learning to be able to sit quietly in a room, alone."
If that's all it was, I would've been happier with it. Being told you create misery, that your love (unless you follow the path) is shallow, that your ego will disappear, being told that Buddhism is 'scientific' and then being told the smallest particles in the universe are 'kalapas' of earth, air, fire, etc... wasn't exactly reassuring. I also disliked the chanting (you don't have to do it, but I personally found it off-putting to listen to).
I actually enjoyed practising anapana and vipassana (less so the third type, can't remember the name), though of course you're not meant to enjoy it. Becoming aware of the extra sensation you have of your body was pretty interesting.
If the path you've chosen works for you, great, but please open your mind to accept it might not work great for everybody. One of the saving graces of the vipassana course for me is they didn't expect you to believe what they were saying, but rather believe in your own experience. That sort of honesty I can respect.
"I was worried that I'd done damage to my brain" implies that you believed your brain was at risk from meditation. You continued through the course, and yet your brain still functions. You assessed the risk to your brain as "high", you came out of it (presumably) without brain damage, ergo your threat assessment was wrong.
To put it another way, you were describing your mind state in a point in time which was incorrectly assessing itself. It turned out that you did not do damage to your brain. You thought your brain was at risk, and your own experience showed that you were wrong to assess the risk so highly.
Yeah, I have (strong) disagreements with the discourses - not just the kalapas thing, but the reference to higher- and lower existences, not to mention the dogma of rebirth. It's mentioned in passing, but it contradicts earlier claims of "non-sectarianism". In fact, it left such a bad taste in my mouth I left my first course (5th night). I went back and almost left again, but mastered my anger. The third time I was less angry. Now I just laugh - the Buddha (and Goenka) are just products of their time, communicating as best they can with the tools they have. The core observations, the core practice, doesn't require any of it.
Yes! I really dug this about the Vipassana teachings. They also emphasize that you can "leave out" (per the "black stone in the oatmeal" analogy) any of the intellectual aspects that don't sit well with you.
I suspect that for most of us, just sticking with a regular practice of breathing (anapana) and sensation observation (vipassana) is enough to keep us busy for the rest of our lives, without adding on intellectual components like kalapas, what happens after we die, etc.