I like Guayaquil, and the place has really cleaned up its act in the past 10-15 years. I have walked around the downtown area alone, even at night. Maybe I was foolish to do so, but I didn't feel unsafe.
Now, the events of this past week are a different story, but they are not localized to Guayaquil. The gang problem is countrywide but is most pronounced in its two largest cities. There is a sense that Ecuador is headed off the rails if the government cannot take control of problem soon.
To the OP, you still have two months before your trip. I wouldn't make a decision yet.