I think this situation is very similar to patients with operable brain tumors. To have to make a choice between losing a part of yourself or dieing would be very near impossible. The Doctor made that choice for her, and we can debate whether or not that was acceptable until the cows decide to come home, but it was definitely in character. At least this way she still has the potential to be brilliant, however slim. I for one am glad she didn't die. It leaves the story open for her to return someday, whether it be in cannon, or just the wonderful world of fanfic.