Google is what it is: trying to sift through all that information algorithmically and using some forms of AI so it can extract what humans think is good information. I agree that a good forum that has good policies is getting hurt by some of google's actions, but it's the larger system, not Google. To make an analogy: almost everybody drives and everybody uses roads, but nobody should say: I'm a good driver or I don't drive, I've never been in an accident, therefore I cannot be in an accident. With all the information and intents behind such information on the Internet, and with google as the self-appointed traffic laws, there is still bound to be some collateral damage, sometimes because of how Google tries to deal with the dreck.
As an aside, one can view Google as a just one way of monetizing information on the Internet, competing and co-existing with many other ways. You can also view it as a giant AI algorithm that gets rewarded (advertising revenue) when it finds the good information that humans are looking for and defends itself against others who have other interests.
If you don't care about what Google's view of the internet looks like, then ignore them, and ignore any emails from people asking you to change things on your site for them. Done. Simple.
This issue crops up because people usually do care what Google's view of the internet is and would like to help make it better. Marking links as nofollow and so on is entirely optional: only people who want useful search engines do it, and others don't care.
"Do these requests indicate a larger issue with my site?"
When the truth of the matter is that it's Google's issue. Why does the burden of the cost have to be on the publisher?
This is the 3rd time someone is pointing this out, and it pretty much showcases "Google"'s attitude on this.
At this point the cost of becoming a good source of information has increased greatly to the point that very few publishers with resources can actively manage all the rules and "guidelines" Google decides to throw at the content creators that provide the content that makes the search engine valuable.
I see this everyday in our business as smaller but richer sources of content just disappear on many topics. Blogs, forums and independent enthusiast content sources.
Google has created a one sided ecosystem. That is consolidating traffic to so called "good" sites.
As a long time publisher for a large media company I think it's time to take the internet back from Google. Who care's what Google thinks and does and start building for a better internet.