I agree with JohnRennie's original view - that you should not delete your question - especially if Answers have been posted. Those Answers might be valuable to the people who posted them, as well as to the wider community. They might be better than the Answers in the Question you are duplicating. Comments can also provide valuable information.
Even if no answers or comments have been posted yet, users might be preparing an Answer and it is very frustrating to have done all that work just to find that the Question has been deleted already. (That has happened to me several times on other sites.)
So I agree that by not deleting and heading your question with a note that it is a duplicate, you did the best you could do.
The slight problem with this option is that you take the risk of attracting down-votes, which cost you rep. That is unfair - you should not suffer from doing the right thing. However, I think it might be difficult to alter the site programming to avoid such a penalty without leaving the rep system open to abuse (posting marked duplicate questions to gain upvotes without the risk of downvotes). Also, the cost is small (-2 per downvote) and few downvotes are likely to be cast if the question is already acknowledged to be a duplicate.
I think a tougher dilemma occurs if you realise that the question is actually a stupid one, or is clearly "off topic", hence is likely to (or starting to) attract many down-votes. Should you delete it then, even if no Answers are posted?
I suggest you should likewise mark it in the title eg "Withdrawn - awaiting auto-deletion" but not delete it, and again allow the system to delete it according to the auto-delete criteria.
There is less of a case for doing this, compared with a duplicate question, since you are unlikely to have gotten any actual or pending Answers - just a lot of negative comments. Nevertheless, I think it is best not to delete in this case also.
UPDATE in response to Comment by ACuriousMind :
My view is that, once the Question is posted, other users may acquire a stake in it. For example, those who are typing/researching an Answer, and those who are debating it via comments or in the chatroom. The OP may decide that he/she no longer requires an answer, or that the question is stupid, but that should not be decisive. Others might disagree, suggest edits, and upvote it. If there are no developments within 30 days, the clean-up process takes care of it.
This view is consistent with that expressed by dmckee that the purpose of Physics SE is not merely to satisfy users' immediate needs for explanations, but to build an archive of Answers for future reference. If the only purpose of Physics SE were to satisfy the immediate needs of the OP, then of course the OP should do as he/she wishes, and delete even if Answers have been posted. Furthermore, all questions might as well be deleted if the OPs no longer need them. But if Questions and Answers have value to the Community of Users, then the OP should not have sole control over their fate.
The purpose of marking in the title is to alert potential respondents that the OP no longer requires an answer. That will discourage some (probably most) users from answering. Exactly what is marked (and where) is up for debate. This is only a suggestion.