Because any one of us lay people, if presented with the same facts the airlines would have known at the time of planning their routes, would have deemed it an unacceptable risk. The G2A missile is perhaps a bit of a side issue. Even if that was unexpected, it shouldn't be unexpected that there might have been an emergency - such as a depressurisation - that might have required the aircraft to decend into closed airspace. That would have put it in range of other missles.
Airlines and ATC were perhaps a bit complacent. 'It's always been that way so it must be ok this time'. They didn't do a risk assessment for this particular danger zone. Well, some airlines did.
I'm not convinced of the merits of secrecy in the airline industry. From the top down passengers are told 'you won't understand' or 'you don't understand'... so we don't get told. But I think we've moved on from that now.
This is a bit more of an interesting issue. Should FAA or other regulator approval absolve carriers from doing independent investigation before they press a new aircraft into service? If we accept that Boeing may not even have told airlines about MCAS issues, should airlines have continued to fly that model after the cause of Lion Air became apparent? At least until the issue was understood and resolved?