Although I up-voted your request, because I like the idea of making structures more accessible to the general user base, I would still need some really good convincing that this was necessary, and which cases would actually benefit from it. I personally dislike JSmol and other embedded interactive elements, because from my experience they drastically increase load times for a web site. We all know that even MathJax can be a real nuisance. Adding on to that is probably a bad idea.
The other concern I have is, how platform independent such an embedded element is. If not everyone can use it, then it is not beneficial at all. Again, we have seen that some posts with MathJax simply don't work (don't render) with the apps because of missing support (the used version is far behind). I tried JSmol on my android phone, which works surprisingly well, but it took long enough to load that I would loose interest in the post.
In my opinion, if we would introduce such a feature, it needs to be in addition to a still frame, and you must actively engage in order to load it. In any other case I assume it would just over complicate the site.
On occasion I have used animated gif to show rotations or certain angles of a molecule. This is because on the internet that is easier to make a point. However, if I were to publish similar results/explanations in a journal I would choose a different mode of presentation.
There are a variety of online tools that allow linking to such structures, so feel free to include external sources in your post. For example: Have a look at this fabulous structure of benzoic acid.
Lastly, I certainly would hope that a way to draw structural formulae on the site is going to be introduced before molecular structures. And we all know, this is already a long shot. We have talked about it (on and off) since the beginning of the site, without any significant change in status quo. (We don't even know if it is being considered.)