I disagree with that last one (I mean, you can rule however you like) but I think that one of the intents of the (clearly messy) new stealth rules is worth preserving: The idea that you can leave the cover, and sneak up on a guard, or move to a different position (crossing line-of-sight without anyone seeing you do it. I think these things are a good thing, and intended. YMMV, but I think that it's fine that "stealth breaks when you leave cover" MOST of the time, but it depends on what's happening in the story.
If you're dancing in front of them thumbing your nose, yeah, you just broke stealth. If you're creeping up on an unaware target, then no. But of course, you do what you like.