Yes, the Wayback machine is a non-ideal tool, and could perhaps even come under threat due to lack of funding or legal issues.
I think that copyright law is indeed a huge problem. While copyright law serves a useful purpose in giving content creators a time-limited monopoly to commercially exploit their work (which has the good of encouraging content creation), the ever-growing length of copyright terms only narrowly serves some corporate interests (such as keeping older Disney IP out of the public domain) while being highly detrimental to the public good, since many older, less popular works are doomed to be lost and copyright restrictions only exacerbates the problem of preserving and archiving them. See also: Public Domain Day - Wikipedia
It’s not just 50 years, but I think over 100 years. For such an incredibly long time span, it’s not very practical for an individual to preserve and archive works. It takes an organization, or at least a plan to pass material down to someone else, requiring considerations in one’s last will and testament. With care, I think it is possible to preserve and pass down a collection of physical books to future generations. However, digital content may erode even faster, since one would have to convert file formats probably at least every decade or so, and transfer from one system to another, before various storage media becomes obsolete. Even now, there are collections of floppy disks where people struggle to find a machine that can read them, and software that can process their contents.
It’s disappointing to hear that he had such a reaction. Really he should thank you for notifying him that his content is on the Wayback machine, if he does not wish it to be there (I believe the Wayback machine will take down content upon request by the actual owners).
I think it’s terribly short-sighted of him to be so concerned about his potential commercial interests, when some Sensei’s Library reference might only minimally impact those interests (and perhaps only benefit them by increasing publicity), since pulling his content off of the Wayback machine and preventing other people from talking about it will only help increase the likelihood that his work will fall into obscurity and be forgotten by time. The overwhelming majority of academics that I know, would prefer their work to be shared and read as widely as possible, since they care more about spreading ideas. Ultimately, seeking to grow the audience is probably a better business model, since the popularity of Go in the West woefully below its potential.
I think a solution is to somehow encourage more content producers to embrace concepts like the Creative Commons and new models for revenue generation. To preserve the longevity of content and ideas, they need to be freely shareable, redistributable, adaptable, etc. Traditional copyright laws are very dated tools that create an artificial scarcity incongruent with an age of digital content.