The point of the prosecutor's fallacy isn't that you should ignore evidence, it's that you must include all the evidence in calculations of probability. Swartz' suicide is inductive evidence for the hypothesis "Steve Heymann caused Jonathan James' suicide", you can't just ignore it.
Can you describe the point at which double counting is occurring? My hypothesis is, "Steve Heymann's defendants are more likely than others to commit suicide". I propose to determine with what likelihood a criminal defendant will commit suicide, determine with what likelihood Steve Heymann's defendants have historically committed suicide, and compare the two numbers. How does excluding Aaron Swartz from consideration make my conclusion better reflect reality?