Spoiler Alert! Don't read on if you haven't beaten Mass Effect 3 yet but BioWare UK Community Coordinator Tully Ackland has now confirmed that Commander Shepard is alive and kicking if you choose to destroy the reapers. The quote from the BioWare forums reads as follows:

“You may notice that in the “Shepard lives” ending, the love interest hesitates to place Shepard’s name on the wall, and instead looks up as though deep in thought. This is meant to suggest that the love interest is not ready to believe Shepard is dead, and the final scene reveals they are correct.”

Since the release of the new Extended Cut DLC many fans have spoken out saying they liked the "control" ending where Shepard ascends to godhood but the "destroy" ending now seems to be a more traditional alternative where Sheppard kicks butt and lives to talk about it. Since we know now that the Normandy isn't stranded on some random planet it's completely within reason that Shepard will be reunited with his love interest and get to work helping rebuild the galaxy.