If we accept that your #1 and #2 are indirect questions, then your sentence #2 is fine, as is:
2a. We all wonder who your partner at the ball was.
(There is a slight difference in meaning between #2 and #2a, but that is not really relevant to your question).
With BE, the 'rule' is sometimes not observed, as in your #1, which is acceptable in conversation.
When an there is an object involved, then we are more restricted:
3. Who invited your partner to the ball? We all wonder.
~ We all wonder who invited your partner to the ball.
4. Who did your partner invite to the ball? We all wonder.
~ We all wonder who your partner invited to the ball.
Does that help?
Student or Learner