The real reason is that WhatsApp refused to provide information about a PCC member.

PCC is the largest criminal organization in Brazil. It's involved in several criminal activities like drug dealing and gun trafficking. It was also responsible for "closing" Sao Paulo city some years ago forcing people to stay at their homes as well as killing hundreds of cops ( https://en.wikipedia.org/wiki/Primeiro_Comando_da_Capital ).

The judge tried to obtain the information from WhatsApp for several months but it was simply ignored. Blocking WhatsApp was one of the last options that she had to try to obtain the information.

Here is more information from a reliable source ( it's in portuguese ): http://www.conjur.com.br/2015-dez-16/bloqueio-whatsapp-pivo-...