James,
You are being somewhat disengenuous when you portray yourself as a journalist following the truth wherever it may lead.
I have reread the article and it is quite true that you are careful to mention that the backseater ejection theory is only one of the options. However, the general tenor of your report is such that the average reader would put the paper down with the belief that it was the MOST likely option.
So why did you emphasise this particular aspect? Because it's more dramatic of course, and it sells papers. Add in a bit of conspiracy theory ("Unusually for an incident in which both crew members have survived without serious injury, the identities of both men have been kept secret.") and we have a government cover up!!
Yes, the RAF
PR side handled itself badly, but does that justify writing unsubstantiated rumour?
Face it, James, you're not in the news business, you're in the entertainment business.