She did turned the stone into another form... into energy and like... shrapnel of the remains of the stone. The logic here is that the stones, when they are destroyed in the same universe they are in, the energy that exists in them is maintained and never disappears, it is just dispersed. Infinity Stones are just concentrated vessels where you can control the six ruling forces of the universe, and by destroying them, you're not eliminating what's inside them, you're just no longer keeping that energy contained in the stones.

However, when you time travel and remove an infinity stone from another timeline you're negating that timeline from having access to an important fundamental energetic component of their universe.

Think of this as an hypothetical container of radiation. If you destroy that container, the radiation will spread out, it isn't destroyed. But if you remove the container completely from one place, you're dragging all that radiation from that location. So, two different things in functionality.