Run 26" wheels on a 29er
If you look at bike literature from the early 29er years it was the best thing to buy. There were some issues that showed up after they became common enough for recreational riders. Recommended frame sizes tended to put people on a frame that was actually to large. It seemed that they forgot about the top tube being raised 1 1/2 inches by the larger wheels. Another issue when 29 inch wheels were put on small frame sizes was toes striking the wheels while turning and pedaling. So while a small size 29er may seem odd now they were a one point common. Manufacturers seem to have learned a lesson from all this and now put 26 inch wheels on the smallest frames 27.5 on the less small frames and make larger frames in both 27.5 and 29. All this is just to explain why you have a small frame with 29 inch wheels. The good news is that with the 27.5 boom 26 inch disc wheels are available with steep discounts. I don't see any reason it wouldn't work. It might be cheaper to buy an entire used bike if  you add in tires and tubes. Use the wheels until she out grows them, put the 26's back on the used bike and sell the whole bike for likely close to what you paid for it.