Hi Jaya,
Even after June when you become a BC, your wife cannot apply for her BC as a Spouse of a BC.
She will have to wait until January 2013 (it isn't far off
).
To apply as the spouse of a BC, one does not have to have lived here for a continuous period of 3 years ,but i am afraid that this doesn't apply in your case.
The requirement is that she has to have been in the UK 3 years from the date of application (hence June 2009) but from your post she wasn't. Also from your dates given, i.e. March 2008 - Jan 2010, she has been out of the country for over 270 days in the last 3 years.
She will have to meet these requirements after your BC in order to be eligible (specifically the residential requirements):
http://www.ukba.homeoffice.gov.uk/briti ... ofcitizen/