The easiest way to do that in the system as it is would be just to run a combat with a few minions.
For my ambitions even that would be too much effort. I would like these "skirmishes" to be resolved in at most two rolls per person, with the only real (tactical) choice being whether to expend useful resources to spare yourself or someone else the consequences of a poor roll (which would generally be a surge, HP, or some kind of mild lingering condition, if such can be made to work, e.g. via the disease track.) The idea being, these are meant to be really, REALLY fast--resolved in just a few minutes--but still weighty enough to have long-term consequences.
One would use skirmish rules for situations like:
1. Infiltrating an enemy stronghold where there are many weak guards, which may be cleared out slowly and methodically (but at cost), or left alone at the risk of allowing reinforcements for the later, major confrontations with the leadership
2. Dealing with minor wild animal threats in nature. Most animals don't attack people unless they're desperate or mentally unsound (e.g. rabies), so these fights should not be tough, but they can add pressure or work as a minor time and resource cost linked to a Skill Challenge
3. Any situation where, sort of as you say, one would expect genuinely every enemy to qualify as a minion or mook. E.g. the "clear out the low-level kobold warren" stuff or fighting, I dunno, the occasional gaggle of giant bees at the edges of a giant beehive or something.
4. Situations where the party doesn't strictly care about defeating opponents, just getting away or getting past them. E.g. escorting someone through dangerous spaces, ferrying a valuable item and fending off people trying to steal it, etc. This again demonstrates how these rules would work in tandem with the Skill Challenge rules, since there could easily be interplay between the two.
The overall idea is just to offer a mechanical representation of these "small" fights, the ones that don't represent a
tactical challenge but that can still represent a
strategic or
logistical one.