There are other ambiguities regarding who should keep those logs, ISP or service providers.
Free Whatsapp and facebook does hurt net neutrality. It undermines competition and leads to a division between services that are "free" and the ones which are not, on a ISP level.
That's not what article 2 says, article 2 is a preamble with the intentions of the marco civil and contains no definition of rules nor obligations. The removal of those videos are not based on marco civil, but on other laws and our own constitution.
The problem is not the Marco Civil, but how it is being interpreted. Our judges do not understand what is cryptography. Our population don't understand and doesn't care. People are just upset that whatsapp is offline.