I think it's just systemic of modern day story telling, that questions are greater than answers.
And it's because of this, that writers basically pussy out at the final hurdle, because you've set yourself up for a big fall, you've posed all these questions that have got people hooked into what happens next in the show.
Instead of a paying that off as you go along, you chose to go further down the rabbit hole, by asking more questions. Because answers in their raw form are basically pretty mundane when it's all said and done, usually someone did x for reason y. But with the more and more mystery angle, well shit it could be anything and it's that endless possibility that's exciting.
Eventually, each time you are getting slightly more bizarre, until you get to critical mass point with your audience, literally nothing you can come up with will satisfy 100% of the people because you've become so convoluted/dense, that you will either sell short or shit the bed with craziness.
Selling short is the safer option, familiarity is generally what the people want, I say all the time that I prefer a dark conclusion to a tale, but deep down I know, I loves me a super happy ending. For example one possible, go big or go home option, of the top of my head, was that all humanity/ clyons are engineered by a third party because it's fun to watch them struggle, can you imagine the shit storm that would have caused ?
Actually, that's not even that far away from the ending we got, it's just a matter of window dressing really and God/Alien/ProtoHuman turning up to explain shit.
I see where you're going with the Lost Prophets angle, bit extreme as the ending didn't molest any children, but I get what you're trying to express. I disagree, my counter analogy would be, if a man saves a person from getting hit by a bus, but then later kills a family pet for fun, is the former act now also an act of evil because of the latter? I'd maybe hold fire on the key to city and what not, but not all things are tainted in context with later act, is my point.
For me personally, as someone who mostly liked the ending, no crime was committed at all so both analogies kind fall apart at that point. Opinions are subjective, I never really got why people even like Babylon 5, but to each their own I guess.