The short answer is no. There aren't really any cheap cruises of the Galapagos Islands. Just getting to Galapagos will cost you about $500; while a 3-day tour of the islands will cost around $600. My tip for finding cheap cruises to Galapagos is to be flexible in your cruise dates and look for last minute deals.
Galapagos isn't really a place you can do on the cheap..if money is an issue, it's best that you head over to Isabella on the daily speedboat and stay there. There is cool stuff to do there like hiking up to the volcano, snorkeling and taking beach walks.
There's even an entrance of $100...I guess they do milk tourists for all they have. Then again, if the Galapagos were a cheap place to go to, it probably wouldn't what it is now. You really can't do this place on a budget, but there are some things you can do to lessen the damage like skipping the cruise altogether and off-land activities like swimming with sharks and see lions.
The best way to get a good deal is to get to quito a few days early and check for last minute tours. I met a couple of people that got 50% off on the regular tour price. Having that said I agree with the post above that Galapagos is not a cheap place to visit.
Visiting the Galapagos Islands might be expensive, there’s no doubt about it. But they’re totally worth it. You can plan your trip during April & May or September & October if you need lower prices. About 2 years ago, we booked Tour Package 4Days/3Nights to Santa Cruz Island & Isabela Island for $540 per person. You can search through the internet and find the cheaper price packages.