I agree with SJOGuy. I have spent a little time in Guayaquil and have friends there. It has a lower homicide rate per capita than a number of major US cities, including Baltimore, Detroit and New Orleans but I dont hear any stories of folks saying don't travel to or leave your hotel in those cities. Personal security for US and western European tourists, especially business tourists, is exceedingly common in many cities all over the world. Well-to-do residents in every city everywhere around the world have security around their homes. My in-laws (civil engineer and a private school owner) in Mexico have never had a problem but also have bars on the windows and 8-foot walls with electrified barbed wire and glass on top - and they live in a gated community.

The troubles in ECU are significant. And since they are prominently on the news it seems to define the country. But this is as close to the truth as the US being paved with gold and everyone has multiple machine guns in running gun battles.

Definitely wait until your cancellation drop dead date. Even then, you are going to the Galapagos so how much time will you actually be spending in GYE? Probably not more than a day or so. If things stay as they are, the likelihood of being involved in anything untoward is very, very low. Just like going to Chicago, or Washington DC, for a day or two.