Yes, too extreme, I think. Your sand hosts a lot of nitrifying bacteria along with your filter, so removing it will remove a good portion of that bacteria and may temporarily worsen ammonia issues. If it were me, I'd leave the main tank running as is, testing and doing water changes until the ammonia issue is sorted. You could try sifting through the sand to continue removing fertilizer beads too, and get some floating and/or stem plants to help absorb the rest of the ammonia faster.
I'm so sorry that such a freak accident happened
The pH increase could've been due to a number of factors, whether it was a simple slip-up in dosing the buffer/minerals, or as you mentioned, potentially something strange going on with the RO water itself. Either way, don't beat yourself up over it. You were already in a tough position with the ammonia and that was a water chemistry curveball in and of itself. You were doing all you could to resolve the issue. Rightfully focusing on the ammonia and doing frequent large water changes inherently leaves a lot of room for other issues to sneak in, with large swings in parameters that aren't easily controllable. You were doing your best (especially after the treatment for your back!) and I'm very glad you were able to save some of your fish and that the ADFs didn't seem to be affected (I wonder if it's because they don't have gills?). It seems like you've been able to stabilize your fish in QT, so I think just put your focus on getting the main tank back up on its feet