Is it permissible to deal with a mediating advertising company if it is discovered after a period of time that my advertisement, which contains no Sharia violations, has been published on a pornographic website among the websites where this company publishes?

It is not permissible to advertise on pornographic websites, even if the content of the advertisement is permissible, because this violates Islamic law. You must ask the advertising company not to publish your advertisement on pornographic websites, otherwise, seek another means.