Years ago, my first attempt of growing a fruit tree in a container was a Meyer lemon. It was infested with scale before I knew what was going on. I didn't use anything toxic to fight them, but what I used didn't work, and the tree eventually started to look like it was on it's way out. I put it outside and sprayed it with the hose, many of the scale came off, this really didn't matter. It froze pretty hard that night and I forgot to take the tree back in(I don't know maybe I had given up).
What I learned is that this killed my tree, but it also killed every one of the scale bugs on the tree as well. Was there any form of scale still in the soil, I don't know, I tossed the soil and started over. The point is, maybe you could put the infested tree out for a freeze treatment. Granted, I don't know if your tree is still very small, or has green wood on it, if either is the case then a freeze is probably a bad idea.
Maybe this is helpful.