As much as I don't agree with you... Let's Encrypt isn't actually an EFF project, or even majority EFF funded. One developer is provided by the EFF, one of the board members is from the EFF, one member of the technical advisory board is from the EFF, and there is a sponsorship from the EFF. The organisation has various other employees, board members, and sources of funding. Even in the genesis of it, it involved three non-EFF people and one EFF person.
The suggested client, CertBot, is an EFF project, but there's a wide variety of alternatives - https://letsencrypt.org/docs/client-options/