There are really two separate arguments here. One is whether the study's conclusions are accurate, and the second is whether they would be acceptable if they are accurate.
On the first question, I'm skeptical of the methodology used in this study. For one, I think family members of high ranking terrorists fall into a grey area and should be counted as a third category. The DOD probably has much better data but I doubt they will release anything.
On the second question, I certainly would not consider 49:1 acceptable but as a said above, I am very skeptical of this number. However, I do believe that special ops and drone strikes are essential to keeping us safe, and are preferable to the alternatives which are increased domestic security and full scale occupations of countries that harbor terrorists.