In some cases, yes, it can be a problem. I tend to think that people will take rep over a badge most days of the week, but they can, of course, get the badge by simply deleting a post - and note that the badge applies to both questions and answers - with a score of three or more, then undeleting it after the badge is awarded. It's gaming the system, but it's possible.
I remember that I earned the Disciplined badge after deleting an answer of mine that involved applying the Tsiolkovsky rocket equation to a dragon (!). It got a few upvotes, but then someone pointed out that my analysis had a flaw, and it turned out that there was another, unrelated error. I couldn't figure out how to fix that, so, even though nobody downvoted, I deleted the answer (and later fixed it, and undeleted it).
Would I have deleted the answer if the Disciplined badge didn't exist? Probably; I don't like posting content that's incorrect, and I'll undo my mistakes when I can. But sometimes, people might not want to delete material, even if it's wrong or flawed, because they don't want to lose the rep - an understandable reaction. The badge helps sweeten the deal a bit; it encourages you to do the right thing.
That's the argument made in this Meta answer, as I just found out. I don't have data (yet) as to whether or not the badge makes more people willing to delete incorrect answers, but it makes sense that it could work. Some might call this a weak argument, and it is, to some extent. But it's a rationale for keeping it, nonetheless, and I haven't seen it used harmfully, in my experience looking through deleted questions and answers.
Also, there are certain criteria under which a user can't delete their own question:
You can’t delete answers that have been accepted.
You can’t delete your own question when it:
- has an upvoted answer, or
- has an accepted answer, or
- has multiple answers (even if there are no upvotes)
We upvote a lot on Worldbuilding, and we get a lot of answers on each question - I think we average about 4.65285663 answers per question, give or take. So it's really hard to delete a question on Worldbuilding once it gets going. This means that it's not easy to abuse the badge, in terms of asking questions.