I think everything happens for a reason. I feel very sorry for the loved ones that lost someone on that flight but my opinion on the afterlife is very different than the Christian concept. Dying is not a bad thing to me, I know that we go on and I don't think that anyone dies by accident. I don't think that those who died on 3407, died as a punishment or that the creator turned it's back on them.
To me the logical explanations are as important as the spiritual ones, It all goes together.
I find it interesting and a bit confusing why some people think that "God's plan" doesn't include those things you mentioned, like the pilot and the weather conditions. I mean, the Divine exists in everything right? Even in us. So we are all a part of the experiences that happen, we all contribute something to everything that happens. We are all connected, intertwined.
Those people who died were meant to go, it was their time. Those who didn't die on the other plane, were supposed to live. Their lives will forever be changed by that experience and each and every one of them were meant to go through that. Some might have received a boost of their faith because they prayed. Others may have realized what is really important in life. Some man on that plane might have realized he spent too much time at work, instead of with his family. So many things may have been going through their minds and so many changes may result from their experience. The deaths on the other flight, may bring other family members closer together. I have seen many things healed within my own family, the catalyst being the death of a family member.
In my opinion, everything is in Divine working order at all times. I attribute what happened on both flights to that concept and I think that concept encompasses rationality and spirituality, mechanics and metaphysics, weather, skill etc., all of it, works in the flow of our Universe and is in sync.
Thanks for asking such a good question. :)