Updated NY Times article - The key word now appears to be "demoted":

"other knowledgeable aides said that Mrs. Clinton was furious when she learned of the Colombia talks and insisted on Mr. Penn’s demotion. Mr. Clinton concurred in that judgment, aides said."

http://www.nytimes.com/2008/04/07/us/politics/07hillary.html?hp

And again the word "demoted" later in the article:

"Although the end of the primary season is drawing near, campaign aides said Mr. Penn’s demotion would change the internal dynamics of the Clinton camp, with a more collegial atmosphere replacing the first-among-equals structure Mr. Penn created around himself."

So he's not really going anywhere. It's all just for visual effects. Penn has been a "loyal" member of the Clinton team since 1996, and the Clinton's value "loyalty" above all else (sound familiar?), again from the same article:

"He remained for the second Clinton term and through Mr. Clinton’s impeachment trial, demonstrating, among other things, one of the virtues that the Clintons prized most: loyalty."

So there you have it, nothing more than a "demotion" for a "loyal" surrogate.