I don't think it can be done by capturing the middle click, but you could achieve the same effect by changing the script such that the HN submission ID is added

I don't think it can be done by capturing the middle click, but you could achieve the same effect by changing the script such that the HN submission ID is added as a url fragment id or dummy URL param to the submission link. Then another script can be used to check the referrer property of each page loaded, and if it points to HN you could insert an iframe and open the comments link using the submission id in the url.