Geez this was just an example. I know that my solution won't help everyone. What I'm saying is: there are more arbitrary limits in Warcraft III that we have gotten used to. Like the fact that you can only have 12 buttons total on the command card. And I see nobody complaining about that.
What I'm saying is: you are acting like a spoiled child that got a proverbial cake once and now cries that it has been taken away. If you hadn't had the cake in the first place, there would be nothing wrong.
Command button stacking was never an intended feature. It was an exploit abusing missing boundary checking which could lead to potential game crashes and other issues. And it was a very recent exploit aswell. It's not like we used that for years.
The point is: if you build your entire map concept around a bug, maybe it is time to reconsider some design choices? Do you need 9 abilities on your command card? Maybe? But maybe not? I don't know your game. Maybe you can try to achieve the same effect that your 9 abilities have with "combo"-like abilities that get replaced after you use a different ability? Or maybe you move spells that are situational elsewhere?
Get creative, guys! When there's a river crossing your path and the bridge is gone, you can still use a boat.