I know nothing about unrest in Guayaquil. Keep that in mind with what I say.

We flew from Quito to the Galapagos, spending a couple days in Quito first. We found Quito interesting and sufficient sights to keep us engaged.

We returned from Guayaquil, spending a couple nights in Guayaquil. There was little of note to see there.

The link below says that some of the Quito flights go via Guayaquil. Ours did not. Still, is there any issue at the airport? Are you able to transit the airport without going into the city?

https://www.galapagosislands.com/tra...n/flights.html