Here's my suggestion. If a moderator is actively unlocking a topic that follows the auto-lock rules (via the web), pop up a message indicating that the topic was locked per the rules, and does the moderator wish to exclude the topic from the rules, Yes/No? If No, then it will lock again later that evening. If Yes, it will be excluded from the auto-lock.
If this is being done by email commands, a message could be sent requesting the same answer. If the moderator doesn't respond, that's treated as a No.
If this is being done by API, there could be an optional setting to make it permanent or not as part of the request. If not specified, it defaults to No.
If a topic is excluded from auto-locking, a nondescript message would indicate this when a moderator with locking privileges views the topic on the web, mostly to prevent bug reports ("Hey, why isn't this topic being auto-locked????")
I think that will be the friendliest way to do it. It could also use a #noautolock hashtag, but I don't want to encourage hashtag pollution.