I have generated most of my wallets through brainwallet.org.But the address that got hacked was the only that I used to create a transaction via brainwallet.I don't remember my passphrase since I was just smashing my keyboard writing random characters for about 10-15 seconds it must have been at least 50(though I think it was more than 100) random nonsense characters.I then just copy the addresses and private keys to a notepad and forget the passphrase forever.I am almost sure it has to do nothing with the passphrase.
I think that if what you are saying is true, then it is possible that brainwallet.org was a scam site all along and was storing peoples passphrases.
Brainwallet.org then used the "brainwallet cracker presentation" as an excuse to shut down, steal all users BTC, and cover their tracks.
They can just claim now that someone has used the cracker program and your passphase wasn't safe enough.
For the record, any user making brainwallets,
make sure you create them on offline computers if you are using any sites' source code.