The problem with these conspiracy theories is that the bitcoins held by Coinbase do not belong to the customers in the first place. They belong to Coinbase, who promises to send you bitcoins when you ask for them, up to the value listed in your account.
That's pretty much spot on, and applies to basically any exchange. In case of Coinbase, people tend to put far too much faith in their insurance policy, and thus don't mind leaving their coins in there for longer periods of time. No matter how annoying certain actions may be that people are suffering from, they should not complain as this is what one can expect to happen from exchanges and other services with full control over your funds.
Exactly, you don't have control of your funds if it sits on any exchange. Look at those people crying about what happened to BTC-e, most of them have huge amount in that exchange, however since you don't have total control of your funds in there, consider it gone. I think we should not put all of our life savings in those exchange the risk is too high. Hope we all learn our lessons well.