Out of curiosity: Why didn't Letsencrypt applied for a trademark right at the start? That this happens was quite foreseeable and occurs quite often if people forget to secure trademarks (I know this won't be a popular opinion because most as I like Letsencrypt and their outstanding service)
It's a fair question, though you don't actually need to register your trademark to "own" it, it just provides some advantages and of course reduces the danger that someone will do what Comodo did.
With the situation now, it's debatable but saying that a trademark 'just provides some advantages' is a bit of an understatement.