Sorry, that was a typo- I meant past perfect, as indicated from my previous post. Apologies, in making that mistake I fear have made this all the more confusing:) I'll leave it unedited so it's clear what you are referring to.
As far as the 'would/one day' sentence, both events are in the past, describing someone who has already died. The 'would' indicates the order of the events, i.e he loved the cigarettes before they killed him. We can think about it in terms of what you would say at the time of the event "I know you love smoking(present), but one day it will kill (future)you", or " He loves the cigarettes which will one day kill him." As these events are now both in the past, we must change the verbs to reflect this, as in my example. Without a bit more information about the context, it is difficult to say what the author intended, but I believe the use of 'would' in Sergey's article is in fact this use of 'would' as the past tense of 'will'.
Regarding the PAST (again, sorry) perfect, I think your sentence with the two past simple verbs (the first sentence) is absolutely clear in terms of the order of events, which is why the 'had' can be dropped.
I was bringing up the point about the 2nd sentence because I think it might be confusing to most learners of English, as the way the past perfect is generally taught in this context is that the past perfect marks the event that happened first, which in this case was the riot, and the past simple marks the event which happens second, which in this case is the perplexing. So, using it to describe the perplexing marks the perplexing as the thing which occurred first. As I mentioned, this would be posssible if there aere an event which followed the perplexing, which in this case could be the stopping of the coinage. To me this seems less clear, although not necessarily wrong, because they are in different sentences.