First of all, it's important to point out that deus ex machina is not necessarily a bad thing. The germs defeating the Martians in The War of the Worlds is an example where it works, and the usage there is really part of the point of the story.
In discussing Errand of Mercy, it should probably be made clear that it, too, is arguably only a de facto example of deus ex machina, since there were clues dropped all along that things were not as they seemed with the Organians. These included their immediate knowledge that Klingons were in orbit and beaming down, the unlikely stagnant culture, and their bizarre lack of concern.
Also, although it doesn't look like you claimed it was, just to be clear, Arena doesn't really qualify as an example of deus ex machina on any level. The revelation of the Metrons is still part of the extended set-up for the main drama, in the eponymous arena. Without the contest on the asteroid, the episode has no real story at all. Also, anyone familiar with the story by Frederic Brown indicated in the credits would be aware of the similar device in it.
However, the outcome of Arena was not the Metrons imposing peace. All they did was stop the two ships fighting in their space, and pit their captains against each other in the arena. They would have destroyed the ship of the loser, if the victor had wished it. Overall peace between the Gorn and the Federation was left to be worked out on its own terms.
I agree there are similarities between Errand of Mercy and Sacrifice of Angels. But there are important differences. For one thing, Errand of Mercy is a one-off. Despite a namedrop or two, the Organians basically never figured into the story of any episode ever again.
On the other hand, Sacrifice of Angels stood at the climax of drama that had been building for seasons. There was a great deal of investment in all of the nuances leading up to all out war between the Federation and the Dominion. DS9 had set itself out to be Star Trek's edgier cousin, and spent a lot of time trying to make the case that that's what it was. Also, because DS9 set itself up as being about story arcs, Sacrifice of Angels can't be separated from all the seasons of buildup and anticipation that had preceded it.
Then, as the great battle is about to begin, the show has this epiphany. After all those seasons, it's suddenly time to finally get back to its roots. Assuming we can cope with the whiplash of that, what do we get afterwards, in the remaining time the show runs? Total silliness, such as that involving the Pah-wraiths.
The problem wasn't that the theme turned out to be that war isn't such a good idea after all. That is consistent with the ideals generally associated with Star Trek.
By way of clarification, the problem was twofold. First, what little dramatic payoff we got was all out of proportion to the buildup. That's it being "poorly executed". Second, and moreover, it was all downhill from there, and yet the show meandered on for almost two more seasons. This, what I called jumping the shark, was the actual nature of my criticism.
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