A script by itself wouldn't be sufficient to interface with the GBA via a link cable. Hypothetically you could send software to the GBA via the "Game Link Cable" that in-turn would enable the means to pass the inputs back via the "GameCube Game Boy Advance cable" similarly to how games like Tetra Trackers or Crystal Chronicles function.
There are two massive caveats to this however.
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I don't think the serial mode to send this to the GBA directly from MiSTer is implemented in the core. So you'd need to send it from another GBA... with a flashcart.
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Some one would need to write this incredible niche piece of software, for a very niche use-case and the user would need the requisite tangle of link cables when perfectly adequate Nintendo controllers are already available that are arguably superior to the GBAs controls.
That said if you do already have a flashcart, GBA, "GameCube Game Boy Advance cable" and GameCube controller adapter you can try this software. It kind of does beg the question; if you're looking for a "more legit way" to play your GBA in this way, surely just play on the original hardware?
The GameCube's GameBoy player along with a "GameCube Game Boy Advance cable" and GameBoy Interface/Swiss might also enable controller functionality. You'd also still need a GameCube to USB controller adapter too.
There is another thread on this subject here.