It would be nice if Apple put the app back because they decided the Times' complaint was baseless. If Apple is willing to stick up for developers that do abide by the terms of service and contribute to the iOS ecosystem, that would serve to mitigate the heavy-handedness we've seen from them so far.
If I had to guess, I'd say that they almost automatically take things down if they get a takedown request, which is unfortunately the policy of many hosting companies like YouTube, etc. After they reviewed the problem, they probably saw how absurd it was (especially considering they like the app themselves and featured it at WWDC) and put the app back up.
That doesn't make sense at all. What about the countless other apps that have been taken down? They got tons of bad press over Google Voice and where's that at? Right, relegated to a webapp.
