Does a prophesy change that? Does it make it so that one result is going to happen no matter what the player characters do or influence? Well, probably. I think it depends on where the prophesies come from. Here are a couple of ideas.
Are prophesies just the gods bragging? For instance, if Marina, goddess of the seas, tells her priests that in the year that her constellation overwhelms the planet of blahblah, a new naval power will rise from the west, is she just letting them know that she has a plan in place and is expecting some favorite group of hers to rise to power by that time? I am really asking a separate question here, and it is what is the limit of the powers of the gods? We’ll get back to Marina in a second. In your game world, can the gods actually predict the future with great accuracy? Do they KNOW what the future holds? If so, then I think the world is now limited to what the gods expect will happen and it cannot be changed no matter what the mortals do. Hey, that may be what you want in your game world.
Back to Marina and her “prophesy” - I don’t think that the gods can actually predict the future, so Marina is just showing off. She’s saying, “I’m bringing a new power onto the seas and you better look out.” In this scenario, the player characters could thwart her plans. Oh, that would piss her off, but she doesn’t really have unlimited power that will make her prophesy come about. She can influence things and make miracles happen, but she cannot preordain who will be the most powerful navy in the world.
So without eliminating prophesies all together as too limiting, where can we use them? Well, the gods do like to brag, so that’s one case, but it isn’t actually a prophesy. I do think there can be prophesies like, “You will know the child is my avatar when the white wolf comes down from the mountain and kills the white deer in the kingdom of Oznarnia.” That’s a god telling you what they plan to do and how you will know they did it, as opposed to “On May 16, my avatar is going to kick your ass.” Not really sure how you’d know which child is the avatar, but isn’t that the fun part about prophesies? Leaving them open to misinterpretation is always fun. I do want to use this kind of prophesy, because it isn’t that different from my Marina example. The god is still sort of bragging, but also giving instructions. There can be a guarantee, “I will create a great flood” but it doesn’t say, “I will destroy this city with a great flood,” because someone might find a way to mitigate the effects of the flood. I hope you see the difference.
You might want to figure out how these prophesies come to the mortals too. Do the gods just send them in? Do the mortals go looking for them in smoke and incense? Were they written down so long ago that no one remembers, and if so, why? Why would a god tell you that 600 years from now I’m going to do
Remember, novel authors use prophesies all the time, but that’s because they can. No one is participating in the creative process with them. But you’re a game master. You may have what you want or assume will happen but the players and/or their dice can change that. I think you need to make sure they have that ability. And always leave any prophesies clear only in hindsight.