This is a really unfortunate tangent and not worthy of any time or trouble on your end IMHO. At the very most a footnote somewhere in the site to say that this project is not affiliated with any groups or organizations would be more than adequate.

Any individuals that try to imply that the naming of a proxy server product within a larger software ecosystem indicate an endorsement of the position of an organization with a similar name are displaying pathological behavior and should generally be disregarded.