I like it. Perfectly workable and feasible. I'd add though, that even if the flight crew did activate the countermeasures it wouldn't help. They've lost two engines and are in a stall - too late to close the gate after the horse has bolted sort of thing. Given what you've said Jason, even a birdstrike from a flock of geese/ducks fouling one or two of the engines is more likely than the mechanical failure given in the book.
Your idea for the crash can also more easily lead into a follow up adventure. With the crash location known and the possibility that any crash investigation was hurried due to the war crisis (and the discovery of the empty Strela launchers would provide immediate & obvious clues as to what happened), it may be worth MilGov and/or CivGov sending a team to more comprehensively search the area once they had the resources available.
I know this is well after the fact but I'm working from the position that with the chaos of the war and the confusion following the loss of the nation's leaders, there would be more important concerns than a long term investigation of the crash (considering the Strela launchers provide an immediate answer to the question). A more thorough investigation might be put onto the back burner, something to do later when things calm down. But things never clam down and eventually the investigation, shoved to the back of the list all the time is either forgotten or deemed irrelevant... until someone realizes that something of value may still lie within the wreckage.
More importantly than anything I've babbled on about here, it's a great example of brainstorming adventure ideas. Jason's post built on Cdnwolf's post and I've thrown my 0.02c worth in, we're fleshing out another potential scenario for the PCs.
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