You can still file, but you will have to mail in your return. She was not entitled to file as HOH because you did not live apart the last six months of the tax year. To back up any claim you might have the IRS will want the documents listed in the following links. It is possible that the only one that applies is the dependency link. The more proof you have the better.
https://www.eitc.irs.gov/EITCCentral/static_assets/f886-h-dep.pdf
https://www.eitc.irs.gov/EITCCentral/f886-h-hoh.pdf
https://www.eitc.irs.gov/EITCCentral/f886_h-EIC_2012.pdf
