I shall pose a counter-question. Why do bad things happen to good people? Why do good things happen to bad people? I see no issue with the death of Stephen.
As to "God's will is worked through the conclave", well, I will agree but only to a point. God's will is also worked through the US general election. The fact that God's will is worked through a process is neither informative, nor useful, not particularly significant and I see little ability to draw conclusions based on such a premise.
The conclave is supposed to elect the man best suited for the job, and it is supposed to be something done with much prayer and discernment. But anyone who has an even cursory understanding of how conclaves have worked in the past will know that often this is not the case.
However, as the saying goes "God does not call the qualified, but he qualifies the chosen." Even though the outcome of a conclave can be very human (though often it is far greater than human), the papacy remains protected.
As to Stephen's qualities, well, by an accident of history we simply are not privy to that information. Perhaps his election was something which was not prayerfully done. Perhaps he was intending on driving the Church of Rome into heresy and God felt the best way to stop that was killing Stephen off. Perhaps God thought it better if he served as an active intercessor in heaven. We don't know.