Will I be regarded as academic dishonest if I submit one paper to a conference as well as a journal?
The issue of duplicate publication concerning conference and journal versions of similar papers is a difficult one. What is acceptable to do and what not depends highly on the field and maybe even individual venues. Of course it also depends on the degree of overlap between the two papers.

Whenever you plan to reuse some content in another publication, be sure to make the duplicate publication transparent by stating the other paper in the cover letter, and citing it from within the paper. In general, it will be required that the later paper goes beyond the results of the first paper, and it is important to point out how it does that both in the cover letter and the paper itself.

In your case, from the conference's side it's probably fine since you informed the reviewers about the duplicate publication and they obviously had no objections. However, since the journal paper was not yet accepted, you should have at least checked their guidelines on duplicate publication, or better verify with your handling editor that it is fine to submit a shortened conference version. Maybe you can still do that now, and offer the journal editor to withdraw your conference paper if the duplicate publication in that case is against their guidelines.