First, kudos to you for realizing the need to consult others with more experience in the piano teaching world. It is something that you will continue to do for the rest of your teaching career. It's why most of us are here!
My advice would be, DROP the John Thompson. Yes, a lot of us learned using those bright red beasts growing up and have gone on to do quite well for ourselves, but that's probably in spite of the method rather than due to it. The finger numbers are a huge problem, and it is good that you have noticed your student is relying on them rather than reading the music. Often times, teachers just assume that they are reading the notes and are shocked when they eventually discover other wise.
Now, I'm not going to tell you what method books you should switch to, but here are some places to get started.
Piano Adventures (pub. Faber and Faber)
Celebrate Piano (pub. Frederick Harris)
Music Tree- Time to Begin (Frances Clark)
If you really like some of the repertoire in the Thompson books, by all means, keep them around for supplemental use. But I wouldn't recommend using them as your primary method o instruction.
Best of luck!