As accurate as it may be, it's terrible from a PR standpoint. The grandmother next door will be less likely to adopt its use if she associates it with darkness/nefariousness. You may be OK with it and understand its true meaning, but this isn't about just you.
But why create the friction in the first place? News are mostly about soundbites, do you think that if grandma hears on the news that a defendant is part of the 'dark mail' initiative that she will be sympathetic towards him?
If I were starting a company to provide service for this protocol, or if I were an email provider considering supporting this protocol, I would be much more happy if it were called something other than Dark Mail.
If this really is just a protocol, and not a marketing name, then the main thing it needs to do is be inoffensive and distinguishable. Honestly, I would be much more comfortable starting a company around a protocol named something super-dumb like MURP or another non-descript acronym.
There are probably names that are just as bad for other reasons, but one of the top goals of naming something like this should be avoiding getting targeted as something intended for illegal use.
Nobody's grandmother uses or avoids Gmail because of any connotations of "Simple Mail Transport Protocol", because they never hear about it. Only the most crazy religious people (or the least imaginative trolls) ever get upset by "mailer daemon"
This, if successful, will be marketed as "Gmail's new secure mail feature" or "SparrowSecure Mail.app" or "$ISP's privacy-enhanced mail option", not as "dark mail, the replacement for your smtp imap and pop3 service".
