It is too early to say now how the Rio olympics will go, so making judgements now would be rash. Who knows what the future holds for Rio and the rest of the world, there is no reason to say they will not get the olympics again, it will probably be slightly more difficult for them because of current troubles, but in 30 or 40 years that shouldn't be too much of a hindrance, and you should be judged on merits at that particular time.
I don't think that Rio will end up getting the Olympics again, even if there are no more major disasters. There have just been too many issues already before the games have even started. Everyone is terrified of the Zika virus, the tropical climate is brutal for athletes, and there have been major problems with the functionality of the dorms.
No, Rio will probably never host the Olympic games again. First, any town that has received the honor in the past falls way down on the candidate list for subsequent years. Secondly, the dire costs of the Olympics will make the local population hesitant to take on massive debt again. Thirdly, as long as Brazil is plagued by corruption, crime and unchecked health hazards such as the zika-virus, it will remain an unsuitable Olympic host for safety reasons.
No, it does not seem likely that Rio will host the Olympics again. In addition to the numerous problems, there are just a lot of locations wanting to host. The chance of Rio having another opportunity does not seem likely, but who knows? Many things that seem impossible turn out differently.