I'm not gonna pretend to be an expert on the GFA but I don't think those terms would have been politically viable. Unless I'm reading it wrong your suggestion leads to one of two potential scenarios.
1. The GFA can be rendered void if the UK and a NI majority vote in that direction.
Why would nationalists or the Republic agree to these terms? The nationalists required the GFA to guarantee a degree of protection
from the UK and NI majority. Agreeing to them having the power to revoke the influence of the EU on issues like the border and justice would surely be an immediate non-starter? I can't imagine the Republic would have been any more agreeable to this scenario either given their current views on relationship between Brexit the GFA.
2. Any decisions like Brexit that might impact on the GFA must receive the approval of the Republic of Ireland.
Would the UK or unionists have been happy to surrender that sort of power to the Republic? Especially in the broad terms that would be required to ensure the Republic agreed? I very much doubt it as it would be a pretty extraordinary thing to do. It would certainly run against the "take back control" narrative of Brexit itself. Plus even in this scenario, the suggestion that the UK
might want to leave the EU at some point would have been an issue for nationalists.
The GFA left us with a NI that was technically part of the UK whilst still kinda/sorta part of Ireland, whose citizens could be both British and Irish and who were allowed seemingly contradictory freedoms, protections and potential political futures. This was only really possible because various factors (such as EU membership and improved relations between the UK and ROI) made so many of these contradictions irrelevant. This was the magic that made the agreement work; double-think and sidestepping issues. I rather suspect that any practical measures that might have safeguarded against the current brexit crisis would also have undermined the constructive ambiguity that allowed the GFA to function in the first place. It was impossible for the GFA to address these questions because it fundamentally relied on these questions never being asked.
Or maybe I'm wrong. Who knows?