Yes, I am totally fine with the entire human race living under such a system if it means we survive or at least have a better chance in comparison to, for example real life where the entire species is divided and more prone to killing each other than facing the actual threat.
Your 'solution' is hinging on there actually being any leftovers from either group.
In the event of a SIN/HERO downfall I can already imagine at least in SIN's case a large portion of them just outright die trying to scavenge the dead corpse of its former organization and the rest just escaping away to try and protect themselves.
The HERO goons who are somehow left over (I can only imagine level 3-5 are left) might end up creating their own cliques underneath of any surviving level 5s in a China type deal where they are going at each other's throats to do things their own way...I mean their little voting system they have can only go so far and if they disagree with each other I can totally see this ending up being the case (Warlord Cliques).
Your idea will literally result in far more deaths in comparison to the current regime/HERO.
HERO as it is now is having difficulties with overworking its agents (Nico, Lexi, Clark, etc) to keep combating threats and thats with its current size...now imagine the organization collapses and it does have a few leftovers...do you honestly think a collapsed HERO's remaining forces can do anything on a vast regional scale? Despite all the recruits SIN has many came to that organization to simply hide away from big govt/HERO the moment it goes away they all go too.
They will defend themselves and no one else (maybe in a few cases they'll help others but eh).
There's just well...a lot of sectors that need defending and there just isn't enough to defend them all regionally (again HERO at its peak right now is struggling to do this as its numbers are limited).
My comrade you forget about the best nation where politics and religion worked nicely together....
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Those freaking commies in the peoples republic of China took over such a beautiful combo (Tibet) that somehow worked damn well (of course it caused shit once in a while but the Tibetan religion is a mighty peaceful one).