I still don't think I'd trust it. While it's probably true that they fixed the software to never again produce this kind of error, I don't like the idea of software being used to correct the fundamental physics that the airframe is dynamically unstable. While the software probably does a good job of correcting it under a wide range of normal operating conditions, can it deal with evolving or abnormal operating condit…
Most of the scenarios you're describing are dealt with in a few ways:
1. Building systems with sufficient margin to account for this kind of uncertainty; even with passively stable aircraft, these margins exist. Feedback control typically increases these margins.
2. Extensive verification under a wide range of input conditions; this is more challenging (how can you enumerate every possible failure condition?), but usually boils down to some kind of Monte-Carlo sampling or worst-case analysis when those cases can be identified. Here's [0] a neat paper that does this in a more sample-efficient way.