Is a joint science PhD/JD a bad idea if I end up pursuing academic science?
Interesting question.  There are so many factors to consider, including time, cost, workload, etc.

It does seem though that having credentials in both disciplines can give you both a unique perspective and a means through which you can influence public policy. Forward-thinking academic departments may see that as a plus.  Of course, others could see it as a lack of commitment to pure science, but I'm speculating.

You should consider that the merging of science and law is not uncharted territory. A great example is Vanderbilt's law and neuroscience initiative, funded by the MacArthur Foundation. See 
Vandy Law &amp; Neuroscience for details.

However, Vandy does not have a 'law and neuroscience' department, and I doubt that the law school or school of psychology (housing neuroscience) would specifically look for a candidate with both a PhD and JD.  But, it would certainly fit. This may be true of other institutions as well.