All Olympic bids are accepted in good faith that the winning country will fulfill the promises it made to win the bid. If Rio does not meet it's obligations, there should be a backup site ready. If Rio is permitted to host the Olympics while not meeting the obligations set out, a dangerous precedent is set. Olympics bids have the potential of becoming a series of empty promises. Each country would have little motivation to meet all obligations as there are no consequences.
Yes, there should be a backup site for the Olympics in case the original site becomes unacceptable for WHO guidelines. Moreover, that backup site should not be in Brazil. Countries that host the Olympics tend to reap financial benefits, tourism traffic, and positive press attention from the event. In turn, they have the responsibility to host a safe, fair Olympics. Brazil has not only spent exorbitant amounts of money on the Olympics at cost to its own citizens, it has failed to build adequate housing or provide safe water with the facilities that money built. The WHO would be irresponsible to ignore these conditions. Not only should there be a backup site for the Olympics; the site should be in another country to make an example of Brazil. That way, future hosting nations will adhere to WHO guidelines.
The Olympics should not have a backup site. Although there are many problems in Rio, including health concerns, security, and air quality, it is too late to move the games. Most recently, Rio's air did meet WHO guidelines. In the interest of safety, given the short time frame, the games should be cancelled.
Every time the Olympics rolls around, there are news articles about how the host country isn't going to be ready. And every year, they pull it off and the Olympics are a wonderful experience. Rio met the qualifications to host the Olympics and they will do a wonderful job. It is just fear mongering to accuse them of not being ready on time.