Published paper without advisor's name while receiving stipend from her grant
I think what I did was wrong because my stipend came from one of her grants.


There is no connection between funding and authorship.  Providing funding is never sufficient to make someone an author.  So you have not done anything wrong for this reason.


  What is going to be the aftermath of this?


I cannot predict what your advisor will do.  I can say what they should do.  If your paper is accepted, your advisor should say this is evidence they trained you so well that you are able to do research independently.  This makes you and your advisor both look good.

A good rule for research in general is:  Do not keep secrets.  If you feel a need to keep a secret, it's probably paranoia.