Well it is possible that he will leave sooner rather than later as he is finishing up his 3rd series on the show so its always possible that the Sun article could be true. I mean we have this quote from Matt Smith from Jonathan Ross last week that seems a bit cryptic.
"I am very happy doing it. I do the anniversary special, then the Christmas special. At the moment it’s 2013 and we will see what 2014 holds.”The BBC is being coy also as they have issued a response to The Sun's story.
“Sorry folks but even we don’t know what’s going to happen at Christmas. It’s not been written yet! But Matt loves the show and is to start filming the unmissable 50th anniversary, and the new series starting on Easter Saturday.”
Well I take it like this. Matt Smith will be leaving Doctor Who at some point. They all do its inevitable. When the time comes no one should be shocked or surprised as it is just the nature of the beast and actors want to do other projects. So yes, Matt Smith is leaving Doctor Who we just do not know when yet.