Users should be encouraged to use only the most specific tags relevant to the current question. If too many people are using both superset/subset tags on the same question, then the tag definitions and wikis should be updated to clarify proper usage.
Tags Are for Filtering
Search on Stack Exchange is very flexible, so tags aren’t really for search. Instead, they are most useful for following or filtering specific topics. So, if people are searching for “agile” when they should be searching for “scrum,” then the tag wikis are not doing their jobs or clarifying the useful distinctions between the terms.
Subset/superset tagging causes filtering problems, especially in high-volume tags. A great example is the challenge of searching for pure Ruby questions on Stack Overflow. Many less experienced users there tag their questions with both [ruby] and [ruby-on-rails], even though most such questions are not meaningful Ruby questions because they’re very Rails-centric. Ruby and Ruby on Rails are not synonyms: Rails is a framework built on top of Ruby, but is a superset that also monkey-patches many core classes. Tagging questions with both terms makes it practically useless to follow the Ruby tag on Stack Overflow, because your feed is then filled with a never-ending stream of Ruby on Rails questions.
Instead of simply following the Ruby tag, experienced Rubyists are forced to create Boolean search queries to filter out Rails questions, making the tag close to useless from a UI perspective. While Ruby/Rails is perhaps a more extreme example, I think the same issue applies to agile/Scrum tags too.
Use Tags That Frame the Question, Not Its Answers
In general, a more-specific tag is preferable to a more generic one. While there can be edge cases, a question about Scrum is not the same as a question about generic agile practices, so having both tags on the same question rarely makes sense. The reverse is also true: a question about agile-in-general might benefit from a Scrum-related answer, but is almost never seeking a Scrum-specific solution.
Questions should be tagged based on the OP's specific context and cognitive framework, not based on the answers a question collects. Tags should be informative and contextual, not aspirational or (in most cases) retconned.
There are always edge cases, so people should use good judgement. In general, though, generic tags should be avoided when a more specific tag exists.