E.J. Dionne in the Washington Post has made the same observation that commentators Keith Olbermann and Chris Matthews have made on MSNBC: the McCain campaign is carrying on two different campaigns. The campaign being carried out by Palin and other McCain surrogates is aimed at smearing Obama's character and building hatred and doubt by linking Obama to so-called "domestic terrorists."
The campaign conducted by McCain himself at the debate was focused more on the issues, with minimal smears on Obama. Dionne seems to imply that it is due to the 'real McCain's' honorable nature that we didn't see the personal attacks in the second presidential debate.
A question raised by commentators on the debate was why McCain was unable to bring up to Obama's face the character issues Palin is engaging in. Is it indeed because McCain is unwilling to sink to such low tactics? Or is it because McCain is aware that there is significant blowback to such attempts? One suggestion was that McCain is saving his character assassination weapons to use as a last resort in the final debate.
UPDATE: Check out this great piece in the Seattle Post Intelligencer about guilt by association called "The Day a 'Terrorist' was a Guest in my Kitchen," by Joel Connelly.