What an interesting conversation this has been. Well, the upshot is I've learned a lot about the word upshot.
The dictionary conglomerate OneLook gives this definition for upshot: a phenomenon that follows and is caused by some previous phenomenon. Macmillan reads: the result of a process or an event. Merriam-Webster1 says quite simply, the final result : outcome. The OED2 offers words such as an end, completion, climax, result, or conclusion, and gives examples of it being used in positive, negative, neutral, and yet-to-determined contexts:
The upshot of all was, our Lord vanquished the devil.
The upshot was, that I found myself overwhelmed with debts.
Suppose a man was to talk in that manner when he's doing business, what would be the upshot?
In short, the dictionaries are conspicuously mum about whether upshots are usually good, bad, or indifferent.
Which brings us to how the word is used in contemporary contexts: literature, journals, magazines. To address this, I offer three links:
You are welcome to scroll through those pages if you don't want to take my word for it, but the upshot is, the word is used much like it's defined. Be it in the realm of economics, religion, law, sports, international conflict, evolution, or just the hardship of humans trying to eke out a living, some set of circumstances comes to a head – whatever falls out at the end is deemed the upshot of the affair. Out the tens of thousands of possibilities found within those three links, I'll offer just one (a scientific use, and a very fitting one at that, since all this research has made my brain hurt):
And because the emissions of the various inhibitory neurons will not be in step with one another, the upshot will be inhibition that can last for a few tens of milliseconds. (Rodney Cotterill, Enchanted Looms: Conscious Networks in Brains and Computers)
Which brings us to the last question that the O.P. asked: What word is used for negative outcomes? Well, obviously, upshot will work fine, although that word can be (and is often) applied to decidedly positive contexts as well.
For alternatives, you might consider: disaster, debacle, catastrophe, calamity, setback, or misadventure, words with meanings that connote decidedly negative outcomes.
1No link given; too many ads.
2No link given; subscription only.