Who did benefit?
If Russia murdered 1,000 innocent people in retaliation for smuggling, how would Sweden, the USA, the UK, Germany, Estonia, Israel, Carl Bildt, Bill Clinton, the CIA, MUST, KSI, MI6, and so many others benefit from covering that up? You claim it would have been some kind of political disaster if the smuggling was revealed, but how?
I am confident that in the West, only the tiniest fringe of pacifists and dissidents would have objected to the smuggling of Soviet tech by intelligence agencies. That is exactly the sort of thing that the public expects their intelligence services to do. On the other hand, the public would have been outraged to learn that Russia had committed the unthinkable atrocity of murdering 1,000 innocent people over the smuggling. I can guarantee that only the fiercest anti-government types would have put any blame on Bildt et al. for Russia's crimes. In fact, if Bildt had revealed the attack and made some kind of "We stand strong in the face of this unprovoked attack!" speech, people would have rallied around him.
On the other hand, if Bildt et al. helped cover up the murder of 1,000 civilians by a hostile foreign power, then that would likely have been the worst thing any of them ever did. If the public ever learned they covered up 1,000 murders, they would have been disgraced for all time with no possibility of redemption. And if the wild stories you are telling are true, there are millions of ways for the truth to have come out, especially with Bildt leaving office shortly after the disaster.
So, by lying to cover up an attack, Bildt stood to gain absolutely nothing and lose absolutely everything. Cui bono? Good question.