I emailed the author of the NY Times story and he got back to me:
The reason the headline was changed is that I filed a completely new, analytical take on the Senate hearing that compared Kerry’s testimony to a similar hearing with James Baker in 1990. In no way was there an effort to censor the story. The headline on the news story was on the Web for 8 hours, and the story set the tone for the media coverage of this issue for the week (see the Israeli government’s angry reaction to Kerry’s comments).
In this era of digital journalism, we almost always file an initial news story, followed by a more analytical story, which runs in the next day’s paper, and the headline is always different to distinguish them.
Thanks for writing.
Best, Mark Landler