I have an easy way! (maybe?)
Ok I'm no modder (wannbe - but a way to go yet), and you guys all know way more about this game than me (so please feel free to squash my idea

)
But it seems to me that you have overthought the problem.
Partisans had little effect on the war - mostly true.
But still, if applied in a simple way they could work and be quite useful? Maybe even fun?
What did Partisans do? Attacked infrastructure! Attack economic assets (IC)!
So how about this: in a region where the occupier is not of the same political alignment as the provence's (natural) alignment and there is no military unit belonging to the occupier in that (or a neigboring) region then there is a chance of a "resistance event". A little scruffy fella (or felless)pops up (you get a warning) and you maybe start to slowly loose IC or infrastructure. If you ignore this - the rate of loss starts to increase.
How to fix it? Move a military unit to that region or into a neigbouring region - no combat - the partisans just "melt away"

They are not a regular unit after all.
But- if you then take your unit away again -

you get the idea. Occupation is a bitch.
What about if you completely ignore partisans? (Maybe you don't want that provence no more?) Left long enough (they eat up enough IC maybe??) they become a regular (milita) division and take the provence for themselves. Then they start acting just like any country again.
Note I said
the occupier is not of the same political alignment as the provence's (natural) alignment
that means that you could have partisans in your own country

Bloody rebels!
O.K. now the interesting idea I saw in another forum comes in "Resistance Doctrine" sorry cannot remember who's idea that was
Good idea though - and historically true. Britain did incourage resistance movements (it is still done today). Maybe you could set it up so that a country can research "Resistance Doctrine" and then foster resistance in the occupied territories of an enemy? (Simply increase the chance of resistance events happening? - or maybe make them appear and 'take' an IC regardless of how near a military unit is?) Don't know how you would 'target' this though??
Now this goes further - (and please no political hammering here - I'm only passing on what I have read)
How does it go? "One man's terrorist is another man's freedom fighter."
So "Resistance Doctrine" is a double edged sword. If you do it to an enemy - you increase the chance they will have 'resistance events'. Then you liberate that land - but there are people there who are still not happy (and they know what to do about it) - so you now have a chance of 'resistance events' continuing. Bugger

Maybe they even 'migrate' across the world by themselves given enough time?
I don't know if this is technically possible in HOI?
Personally I don't want to be attacked by scruffy goat hearders - I want to be attacked by PARATROOPERS ( and lots of 'em !!! )
Because "They do not like it up them, Mr Mannering. They do not like it!" A bad misquote of the Corporal from "Dad's Army"
