In the comics the Infinity Stones only work in their own home universe. When they are outside of this home universe they're still glowing objects, but they lack the power to affect change on a significant scale, even when wielded by a powerful user or embedded into a gauntlet.
This, presumably is why the Infinity Stones at the TVA are treated as little more more than paperweights. Once their home timeline has been pruned, the stones no longer have any power and hence can be treated as mere baubles. There's also no risk that someone from the TVA could grab one (or all) of these stones, head back into the prime timeline and set themselves up as a god.
