It's a common question in people's minds, particularly those lovers of the natural world to whom the Galapagos Islands is likely to be a dream destination. The answer we would propose won't surprise you (it's 'yes') but we will set out some reasons which hopefully back up what we're saying.
Yes, you should visit the Galapagos but only if you do it well. That is to say, go for a proper amount of time - a week at least. Every plane travelling to the islands brings with it risk of transmission of invasive pests. The authorities have a good handle on this stuff (you get fumigated on the plane before you leave the mainland!) but nevertheless, the chances of something making it through simply increases the more flights there are. The shorter people's stay in the islands, the greater the number of flights.
Longer stays also tend to imply that people have time to disperse more widely across the archipelago so you get less crowding. In fact, the National Park authorities are world leaders in visitor management - live aboard boat licenses are limited to just under 100 with no new licenses issues (it's one out, one in). Each boat is permitted to land in any given visitor site only once every two weeks - that is to say that boats are effectively on a 14 night circuit of the islands (most/all of them split into week A & week B itineraries). However, not all the islands are national parks so it is possible for someone to fly out to the islands, spend the night in Puerto Ayora on Santa Cruz and then fly back again next day having never been in the national park and having done nothing for the island economy.
We love Galápagos Island stays (as in, staying in one of the towns/villages), they give you the chance to experience life in this extraordinary place. However, they work best when combined with time on board in more distant parts of the archipelago. This is a way of creating benefit for locals and for the national park and ecosystems.
Finally, eco tourism brings benefit to the Galápagos Islands. Back in the early 20th century, the California Institute sent an expedition to the islands to capture one of every species. Essentially, they wanted to create a snapshot of the species diversity before humans destroyed and killed them all off. A hundred years later and over 95% of those species are still in the islands. Not necessarily safe and well but they are there and protected by the fact that tourism, well-managed tourism, ensures that the islands are worth more intact than destroyed.