Are you thinking of proof by contradiction, which is rejected by constructionism?
[Dis]proof by counterexample is the most straightforward way to show a statement to be false. What better way is there to disprove a general statement like 'all x are y' than finding an 'x' that isn't 'y'?
It’s very straightforward, but it often doesn’t (and here didn’t) fully satisfy the curiosity that was embedded in the original problem. Why did the Jacobian conjecture seem to be true? Is there some underlying symmetry that’s very slightly broken? Or perhaps there’s all kinds of counterexamples, and the intuitive pattern is only real for certain kinds of functions which happen to predominate in our intuition. Then how should we adjust our intuitions to better capture the space of possible polynomial functions?
You, right now, have the ability to spend a few weeks studying the Jacobian conjecture and its counterexample and write up a blog post about what you think is special about this counterexample.
Those are all good questions, but I don't really understand what alternative you or the OP are looking for actually resolving an untrue conjecture, besides a counter example.
I would frame it differently. The existence of compact counterexamples to a true-seeming conjecture suggests that there’s some deeper understanding waiting to be discovered. Fuzz testing for theorems, if that makes sense. I hope mathematicians in 2036 will be able to explain in detail why the Jacobian conjecture was false and identify which similar, true conjectures the community’s intuition was pointing towards.
We can take a simpler example. Let's say someone conjectures that all linear maps are isomorphic if they have the same domain and codomain*. A counterexample is easy to find, but true insight would be to notice that all linear maps with the same domain and codomain that are not isomorphic map some non-zero elements to zero. That is much more interesting than just finding a counterexample. Although, that isn't to say that finding a counterexample is not very interesting.
*statements only apply to maps whose domain is finite-dimensional
I suspect an AI, possibly a successor to current LLMs, will achieve that by the early 2030s. It might help illuminate many mysteries in math and beyond for us all.
There are many cases where it's possible to prove that counterexamples must exist, without identifying a specific example. This kind of proof provides more insight into the problem than simply finding a counterexample.
Constructivists would surely disagree!
Isn't the fact that you now know that the conjecture is false a huge help? At least it will help convince people to look at the conjecture more closely, no?