The data in Webmaster Tools has been historically unreliable[1][2]. If you compare it to data in Google Analytics, the two have often been world's apart. Sadly, this isn't going to come close to replacing accurate keyword data in GA.

[1]http://www.portent.com/blog/analytics/google-webmaster-tools... [2]http://moz.com/blog/comparing-ranktracking-methods-browser-v...