How do people cope when they want to run apps in AC & DC mode?

Before syncing, go in and stop any applications running from the music partitions. Or make sure your applications don't run from the music partitions.

Is the answer just to disable the integrity check in Hijack?

No, that only takes care of the mandatory fsck after X numbers of rw mounts (ie prevents you from getting the fsck delay when you really just wanted to toss on a few tracks and are in a rush to go...) If something happens that really requires an fsck, it will still happen - ie it's safe to use the Hijack fsck disabler.

/Michael