Update: From what we're reading, it sounds like what the NYT is really complaining about is that its feeds are preloaded into Pulse, and that Pulse is using NYT content and images in its promotional materials, not that Pulse is a paid app. Seems like those are easy fixes -- we'll see what happens.
Update 2: And it's back! As we guessed, it looks like all Pulse had to do was resubmit without preloading the NYT's RSS feed and take some new screenshots of different sites, so that's just peachy. Still, it's insanely troublesome that Apple's first response is to just pull apps without verifying any claims or allowing devs to respond -- your store is still broken, Steve, no matter what percentage of apps you're approving.