I've heard this idea a few times before and it sounded ridiculous then. I think it's nothing more or less than a misguided cultural meme - something that people by saying repeatedly to each other have perpetuated, and filled with a life of its own that bears no relation to reality. I get the impression that it was invented, somewhere, by someone, because it seemed plausible (or just because they wanted to find something to be offended about, probably on someone else's behalf rather than their own). It continues to be perpetuated because most people don't have epilepsy themselves, therefore tend to take on trust the assertion that since epilepsy IS essentially a storm in the brain, brainstorm is a word that can refer to it. Thus, the presumption goes, it would be reasonable for people who had epilepsy to feel think that their condition was being made light of, and so feel offended by the word being used in another context.
This belief is undermined, however, by the simple fact that "brainstorm" simply isn't used to refer to seizures, by anyone, and so far as I know never has been. The only time I have ever heard of the word "brainstorm" being in any way associated with seizures is in the context of this particular myth, which I think says it all. "Brainstorm" has a clear meaning already, which epilepsy sufferers are just as aware of as anyone else, and know it has nothing to do with them - so why in the world WOULD anyone feel offended by it?
Personally, I find the only insulting thing here to be the implication that Epilepsy sufferers do not share everyone else's understanding of the English language, or alternatively are so paranoid and defensive that they have nothing better to do than go round getting upset at things that are not directed at them. Now that is rude, albeit probably due to ignorance more than an intent to patronise. Maybe if it bothers your dad's HR manager so much he needs to find out what actual epilepsy sufferers think, instead of assuming he has the right to speak for them.
Since the subject came up in this thread, I thought I'd address the use of "Epileptic", "Diabetic" etc to refer to people with those conditions. I'm actually opposed to these terms because of what they imply. They tend not usually to be used as an adjective but in their noun form, with the unfortunate effect not of explaining, but defining the person.
There's a big difference between saying "Sam sufferers from epilepsy" and "Sam IS an Epileptic". In the latter case epilepsy, which is simply an illness Sam suffers from, has become elevated to the defining feature of Sam's existence, and reduces him from an individual human being who happens to have a sickness to a generalisation of sickness that happens to have a human form. This linguistic sleight of hand by which an adjective that describes a little of someone is transformed into a noun that is taken as representative of the whole of them (which incidentally is known as synecdoche, if you happen to be interested) always tends to dehumanise and devalue the individual towards whom it's directed.
Just to be clear, "Epileptic," "Diabetic", "Paraplegic", etc are perfectly valid as straight adjectives. It's perfectly reasonable to speak of an Epileptic Seizure, or a Diabetic Coma. I just think they communicate a subtle disrespect when they sneakily assume their noun forms, and this usage should be avoided if possible.