Didn't the writer mean "scuttle"? he asks, citing Merriam-Webster's Online Dictionary. There scupper is defined as "an opening cut through the bulwarks of a ship so that water falling on deck may flow overboard" while scuttle means "sink or attempt to sink [a ship] by making holes through the bottom" and also "destroy, wreck or scrap."
Under scupper the verb, however, M-W does give the sense "do in" -- a sense that's way more common in British English than American. (And yes, Chris Brummitt -- judging by his appearance on "The PBS NewsHour" -- speaks British English.) A Nexis news search returns just three uses of scupper in the past month in US newspapers and wires, versus roughly 400 in UK publications.
Scupper has somewhat murky origins, it's true. The OED's first sense for the verb is "To surprise and massacre," a usage labeled military slang and dating to 1885. The meaning "defeat, ruin" shows up by 1918, but the first guess at etymology comes only later, with the 1993 additions to the dictionary: "The connection [to the noun scupper] is perh[aps] explained by Fraser & Gibbons Soldier & Sailor Words (1925)," which noted that "A man killed in action or falling in heavy weather would naturally roll into the scuppers."
The 1993 additions also include a new definition of scupper, dated to the 1970s: "To sink (a vessel) deliberately; = SCUTTLE
So in the OED's view, "scupper a ship" is a (fairly recent) mistake for "scuttle a ship." But "their plans were scuppered" is standard usage, nearly a century old.
I'm going to nominate scupper vs. scuttle for Lynneguist's "Difference of the day." Thanks for the tip, Paul!