My wife and I went to the Galapagos in April 2011, and had a great time on a tight budget. Our key was being flexible, and not making specific plans until we got to Puerto Ayora.
It's very counter-intuitive, but you will pay the HIGHEST prices in the Galapagos if you book in advance. This is true for all hotels, cruises, and eco-tours. There are GREAT last minute deals to be found if you're there in person to snatch them up. Just get to town, and start shopping. Note, though, that this strategy may not work in "high season" when everything is truly booked solid.
Our plan was to find an affordable hotel as our "home base" in Puerto Ayora and schedule daily trips from there. Since April is relatively slow, we were able to arrive without a reservation and browse around town until we found a hotel we liked at a great price.
Our "friend for life" in this regard was Jenny at Moonrise Travel in Puerto Ayora:
Galapagos Moonrise Tour Operator
Jenny is a saint. She really wants to help people have a great time in the Galapagos, regardless of her booking commission.
During our stay, she hooked us up with a friend of hers that runs a no-name hotel above Galapagos Deli (I sure hope it's still there). We got a top floor SUITE with bedroom, living room, kitchen and patio overlooking the harbor for $60US per night.
Outside the hotel
Living area
View from our room
Right down the street, the "big hotels" in town were charging $200 and up per night for basic double rooms with no view.
We did dive trips nearly every day, but since your wife's not a diver, I'll skip our (extensive) dive recommendations. Jenny can help your wife schedule any of a number of eco-tours (we liked the slightly more upscale trip on the Santa Fe). She might even be able to book your wife on a non-diving liveaboard trip for a few days.
Galapagos is an amazing place. I hope your wife has as great a time as my wife and I did.
