I fully support this for beta and other sites with a small user base, though I do think the auto-clean script should continue to be run on SO.
Here's the issue:
SO has 1.5 million users. When a tag doesn't get used in six months, that means the tag is niche and a tag is probably not necessary.
Beta sites often only have a few hundred users. For instance, Biblical Hermeneutics has only 761 users as of today. If you factor in the size of the user base, that means that a tag used only once on BH is equivalent to a tag being used 1,971 times on SO in six months.
The problem is not that the tag is a niche topic, but that the user base of the site itself is small. We should encourage the use of tags in order to attract a larger audience. (If you're not aware, tags are useful in SEO because they appear in the page title, and thus appear higher in search results for that term).
You could argue that the tags are niche because the site topic itself has a smaller audience, but this logic is wrong. Are there really only 761 people out there interested in the Bible? This site, which I have no affiliation with, along with many others have a very large potential. Anything we can do to increase the user base on small SE sites should be encouraged.
Instead, I would support a review queue for infrequently used tags on smaller sites. This allows a community to prune its own tags at their discretion.