Indeed, I'm as puzzled as you are, because chemistry deals with chemical reactions involving bonding of atoms via convalescent electron sharing. So, such reactions have nothing to do with what Rutherford was doing.
In justification of that 1908 Nobel, they said the price was "for his investigations into the disintegration of the elements, and the chemistry of radioactive substances" (my emphasis) which sounds like a complete misunderstanding, because radioactivity results from changes in the nucleus and convalescent electron bonding has nothing to do with it. The only explanation of such misunderstanding could be that back in 1908, most people incluging Nobel Price Committee did not fully understand what nuclear physics was about. In fact Rutherford is described as "the father of nuclear physics", so I guess the proper discipline in question herein, was established a little bit later. after Rutherford's achievements were digested and classified, maybe even after his death. Rutherford's contemporaries didn't know much so they naively imagined Rutherford's science was about "substance transformation" like in chemistry.