Threat model, threat model, threat model. There are some people for whom "The government is literally after me, personally" is a valid threat model. There are some people for whom "Google employees with privileged access to Gmail are conspiring to be after me, personally" (one assumes there's a two-person rule for access to individual inboxes or deploying code that scans inboxes) is also a valid threat model. However…
To my knowledge, it was Flame that did this not Stuxnet, and it was an attack on MD-5, not SHA-1 [1]