Not necessarily. It is implied that natural energy was much stronger back when Groudon and Kyogre went through Primal Reversion for the first time:
I agree that they may have used Pokémon to build things, like the sundial, but what you say could also apply to the Orbs.
I think you forget how the Ultimate Weapon worked: once it was built, it absorbed the life force of many Pokémon, and once charged it was devastating enough to end a war in a single blast. In recent history, it was unearthed by Team Flare and it was shown that it is capable of absorbing all of a legendary Pokémon's power. It is prevented from doing so, but with the little energy it had left, it still destroyed part of the town that had been built around it.
And it was created by a human thousands of years ago. This is why I think it is pretty reasonable (though not the only possible explanation; we can speculate freely on this, as I said) that the two Orbs could have been created by other humans, also thousands of years ago. The Orbs wouldn't even need to absorb all of their energy, only enough to make their battle stop.