Yes, your spouse can apply under her name for the SINP, even if she was previously listed as a dependent on your application. The fact that her documents were used in your past application does not disqualify her. However, only one SINP application per person can be active at a time, so ensure your previous application is officially closed or withdrawn before submitting a new one under her name. It sounds like your immigration agent may be misinformed or misguiding you, consider seeking a second opinion from a licensed immigration consultant or lawyer.