I think the issue lies in the SE team's failure to communicate the issue properly.
If a moderator appears to be acting without community consensus, there should be warnings stating clearly the nature of the issue and the correct course of action to take:
HopelessN00b, I'm becoming very concerned about the recent actions you've been taking. It seems you're acting without community consensus, mass-closing questions without seeking input from the user base at large. Keep in mind that moderators are supposed to act on behalf of the community, not in place of it.
Before making any drastic changes to the site, even if supported by established rules, please ask about it on Meta and, and most critically, have the community play its part. Make sure the community is involved in the cleanup. A Meta post directing the community to vote to close such questions would be a great idea—you would simply work in tandem with the close voters.