Can Apple delete an app installed via iTunes or the App Store without your permission?
Yes, it's true Apple can remotely delete apps. This is a failsafe in case a nefarious app accidentally makes it past the review process. Not sure about Mac App store, I doubt the ability exists there. It's a different installation/update process.

I don't think it's been done before, and I wouldn't worry about it. It's a good thing. I would want an app that say sniffs my credit card numbers or is actually a trojan horse of some kind to be removed from my iPhone post haste.