You can obtain an IDbConnection object from the NHibernate session, and execute any commands using this. The following code assumes that the session object is an open NH session, and runs stored procedure MyStoredProc.
Code:
IDbConnection cn = session.Connection;
IDbCommand cmd = cn.CreateCommand();
cmd.CommandType = CommandType.StoredProcedure;
cmd.CommandText = "MyStoredProc";
cmd.ExecuteNonQuery();
What you can't currently do is run a stored procedure that returns data and map the data to persistent objects.
You also need to be aware that if your stored procedure amends the data in your tables, this will not be reflected in any persistent objects already loaded.