I'm not sure we're getting at the right problem here.
It has been my experience that if I take my fleet somewhere I shouldn't have and it gets wiped, it was probably because I ran into some
honeycombs powerful enemy ships. Those ships then go up on the Threat counter, and are free to come hurt me wherever it hurts the most. If that happens to stack up with anything else bad happening at the time, you get *FUN*.
I think Threat mechanic is really freaking cool and leads to a lot of the "AI impresses the player" moments, and has been an integral part of the game since forever. So if for some reason it's not working as well as it should (too passive? not enough enemies? too easy to manage?), I think we should look into fixing that instead of creating a new thing that is like the old thing, but more blunt.
If we're talking about an even battle that ends in mutual destruction or the player using several waves to take down a fortified position - I don't think it's fair if the AI goes out of its way to kill the player for it, either. The downtime may well be boring in these cases, but it's really hard to patch that with a specific mechanic because a) it has to be something you wouldn't do the rest of the time and b) have marginal fun utility higher that Youtube.
Maybe I'm just used to playing in such a way that this isn't an issue, so would be cool to hear specific scenarios where this is a big problem. Maybe it turns out that the economy allows you to build up a lot of stuff over time, but not replace it. Maybe it's a problem with specifically high-power setups where your resources are tied up in bigger stuff, etc.
For some concrete suggestions:
1) check if Threat is still a threat in moderate amounts, if not - maybe something along the line of Captain Jack's suggestion of drawing extra units from nearby systems would work. Or Special Forces packs beelining to ongoing battles and joining threat. Or adding entirely new and evil behaviours to mess with players who have been perfecting their defensive strategies for years. Point is, this is a strong, core mechanic and there are a bunch of knobs to tweak there, with potentially wide-reaching benefits
2) make sure we are somewhat balancing the Metal costs with the upcoming Fuel costs, so that the player can't get themselves in a huuuuge time hole just by losing their fleet. But we really know nothing about what the economy will be like at this point.
3) don't make tactical defeats game-ending! That just leaves "reload and don't mess it up this time" as the only way to proceed, and I don't think the game will be better for going in that direction.