FWIW, I've been able to book LATAM flights from the mainland of Ecuador to the Galapagos using my AA miles. It's a cheap 5000 miles, plus more taxes than you'd think necessary (about $45 one way). The key was to search inventory on BA and then find a competent AA agent to duplicate it (if you're connecting, encourage them to search by individual segment if they're not finding the flights). BTW, BA's taxes are about 2x AA's, so I guess the taxes are right. My "on request" AA reservation ticketed in less than 24 hours.

LATAM availability isn't great, but I found about 2 days each week with seats when I was looking. I know most people are going on expensive private boat tours, but if you want a much cheaper "land-oriented" Galapagos visit, consider an "open jaw": fly in one direction to San Cristobal (SCY) instead of just Baltra (GPS) to open up more award inventory and save yourself a needless ferry ride.