It's possible. They could gut the whole thing and add completely new show scenes and make it completely unrecognizable.
But they won't.
Not only does history show us this when it comes to similar glorified refurbs of this type, but so does the fact they are doing an "overlay" to begin with. To be honest, with the age of that building, it wouldn't likely be much more expensive to just build a new ride if they were going to that drastically change it. At some point, massive rebuilding is less cost-effective as starting from scratch.
What will likely happen is exactly what is being rumored - an overlay, using what existing elements they can, and doing as little structurally as possible. Given the amount of dark/blank space in Malestrom, I can't help but think it will have a lot of projections - lots and lots of projections, and a few AA's.
You are absolutely right that it could be a lot more - but I just don't see it happening.