Retied accountant here.
This is not a tax return for the Watchtower Bible and Tract Society. It is a form 990, the form used for non-profit entities. In this case, the Henrietta M. Riley Foundation. It is either a private foundation, or a trust treated like a Foundation. The Watchtower is a beneficiary of the trust, meaning it gets the income generated by the trust.
Irrevocable trusts are commonly used to pass on estates to children, or causes the grantor considers worth doing. I assume that MS Riley was some rich JW that got talked into creating this trust. One of the fun facts about this type of trust, is that the beneficiary has no control over how the funds are invested or managed, so long as the trustee is following instructions.
I suspect that in this case Ms Riley's trust document says something like "make money and give it the WTBS," and failed to specify that the trust not deal in things like the military or tobacco. From my recollection of the last time this came up there was more of that sort of thing listed. It is possible that the trustee divested some problem stocks without violating the trust agreement.
I may not be able to get any more information, but I'm going to try next week, just because I'm curious.
I have no doubt that the WTBS has engaged in some questionable practices. I don't think this is one of them.