(I understand you don't agree with our rule. I understand I should be expecting a new SEN policy any moment now, and I look forward to reading it. But, perhaps just for the record, here is the answer to your question.)
We have a documented Skeptics.SE policy that the mods are following: Guidelines for Inadequately Referenced Answers
If [... adding a banner ...] is performed by a mod, they may choose to make the answer "community wiki". This allows more people to fix it, reduces the cost of the downvotes to the author, and makes it cheaper for others downvote.
That is the "official" answer to your question.
To expand: we could either ignore the broken window, delete it outright or add the banner and hope. While I would vastly prefer to delete it outright, the community spoke on the matter and preferred banners to deletion.
The banners are harsher to reputation than deletion: they are practically a call-to-arms for the item to be downvoted. (Yes, the question might be saved in response to the banner, but in practice this seems uncommon.) Under such circumstances, this is less a "reputation denial" mechanism, and more a reputation preserving mechanism.
I hope this demonstrates that these actions aren't mods being petty or "passive-aggressive". Our treatment of banners was discussed between the Skeptics mods, with the community on Meta, with an SEN employee and with fellow mods of other SEs, before we started uses them in the field. We are trying to toe the line between network policy, what the community wants, and keeping the quality of the answers high enough to attract more experts.
