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I suggest you follow the process on the Nominet (the registry for the .uk TLD) complaints page for domain names used in connection with criminal activity. Complaints - Nominet
I disagree kinda with comparing SSL certificates with a "lock". Its more like a business license, like a grocery store license, alcohol sales license or resturant license.
And thus, it becomes more resonable to petition for its removal. However, since Lets encrypt is a "business license" anyone can get (SHALL-ISSUE), it becomes like described in "The CA's role in fighting phishing and malware".
Think like a CCW (gun license) with shall-issue - but more business related. So while you are right that Lets encrypt wont revoke the "shall-issue business license" from the malicious page, its kinda wrong to compare it to a lock.
Well, I agree it's not really a lock, but I also don't think it's like a business license. It's more like the company that provided the house address number sign for the building, so that people could know whether they were at the address they thought they were. But it doesn't really have anything to do with what goes on in the building.
To the best of my knowledge, a CA in no way, shape, or form ever issues a license of any kind to any entity to permit any activity of that entity as a CA in no way, shape, or form possesses the sovereignty to govern the activities of any entity aside from itself via the service it provides based upon associated agreements. Therefore, petitioning a CA to cease providing its service to any entity in no way resembles enforceable denial of that entity's ability to continue performing the activities upon which the petition is based. Such a petition is, to me, little different from a petition upon a mobile phone service provider to cease providing its service to a criminal organization in hopes of halting said criminal organization's criminal activities. It is, to me, an ineffective and subversive approach to DIY law enforcement that walks a very thin line, much like having the power shut off to a neighbor's home because their electric fence is (possibly rightly) perceived as a threat to neighborhood children and pets. In my experience, denial of service rarely prevents crime; it merely shifts how crime is committed.