Depends how much value and money it's worth to you. Are you prepared to go to war with them, or do you just want you objection recorded.
I would contact (not confront) the site owner - I would start on the basis that the original software is not malware, and would like to help resolve difficulties people are having. I would ask for him to update the site with relevant information, and provide proof of his claim that the software is malware (Maybe you app got hijacked along the way, and a "version" does exist that is malware) I would ensure that my "fix" to the problem was linked to and/or provided from the site. I would also ask the site author to inform the readers that the software author had contacted you and was addressing issues.
After reasonable attempts at this (and if I was motivated enough, but likely not worth the effort and cost involved) I would consider contacting my lawyer and having a "cease and desist" letter sent to the site. Depending on the wording on the site, you may have numerous legal claims against it, however, if a simple letter does not work, the $$$ will mount up pretty quickly and probably not get what you want. Even one simple letter will cost $$$, and that's assuming it's operating in the same legal jurisdiction as you do - cross borders and it is hopeless.
An alternate approach would be contact the advertisers on the site, and inform them that the site was making dubious unproven claims that had legal implications. A copy of the "cease and desist" letter could be included.