"All was well until we got an email from the Intercontinental San Francisco, saying that they had determined that our event was in conflict with Apple and that due to their contract with Apple, we couldn’t use the space."
This is very common for hotels hosting conventions - they will never host a second convention that appears to be similar to the primary, and CocoaConf was naive to believe otherwise.
With that said, Apple had an opportunity to win some decent karma by helping out this overflow conference and waiving their contract rights with the Hotel they are booked with. They clearly can't handle the primary volume themselves.
I guess, from a business perspective, they would rather not dilute their conference, even if it means that several thousand people won't get an opportunity to go one.
Of course, without more information on what actually happened, when, and what kind of notice they could have realistically received, this might be a bit harsh. If Apple just kind of swooped in and said "hey hotel, we're going to be using you next month" and the contract required compliance... then it seems like the hotel management has signed a very one-sided and unfortunate contract with Apple (of whom I'm not a big fan but wouldn't blame for this).
Anyway, this is a shame. Hopefully next time they can get a reasonable guarantee on their venue.