defend? yes, but don't exaggerate... you won't lose a registered mark that easy.
i think that Comodo's actions were most likely an aggressive move to prevent ISRG from obtaining a REGISTERED trademark but once that the registration is finalized, if your lawyer keeps saying that you "MUST" aggressively enforce a trademark or you lose it then that lawyer is probably only saying this because they expect a fat paycheck for their "enforcement" actions and in the process they're gravely misleading you.
you must actively use it, yes, and in this case imho ISRG/Let's Encrypt did the right thing, they sent a very polite letter about the potential name confusion and that was it.
The point of a trademark is NOT to prevent someone from the other side of the planet to make the same product but to avoid customer confusion as to which company made which product. You can make related products as long as you don't cause customer confusion about the product or origins of the product. Trademark and copyright have different purposes.
In this case, as far as USA trademark law is concerned, LetsEncrypt.sh did not have to rename, they only had to provide a very visible notice that they are just a community-made site and not directly related to ISRG/Let's Encrypt. They just chose the rename option to make their product to stand out more.
for example: https://acme.com/catalog/
is obviously a humour site and they even have a notice that they are not related to Warner Bros. (That note mixes trademark with copyright concepts, but even so it still serves its information purpose.)
Additionally, the mark-dilution provisions in the trademark law are currently under review because many view them as an unconstitutional restriction on the First Amendment:
https://www.techdirt.com/articles/20160828/22000835373/louis-vuittons-inability-to-take-joke-opens-up-chance-to-fix-our-broken-trademark-laws.shtml
Finally, as LetsEncrypt.sh is from Germany and using a TLD under British Overseas Territories jurisdiction, the USA trademark law doesn't apply here, only international trademark-related treaties can be applied in this case.