Damage reduction is applied to the overall damage the swarm deals
The rules for creature subtype Swarm state:
A swarm has a single pool of Hit Dice and hit points, a single initiative modifier, a single speed, and a single Armor Class. (...) Swarm Attack: creatures with the swarm subtype don’t make standard melee attacks. Instead, they deal automatic damage to any creature whose space they occupy at the end of their move, with no attack roll needed. (...) The amount of damage a swarm deals is based on its Hit Dice, as shown on Table: Swarm Damage by Size.
|Swarm Base Damage
The key is to think of the swarm as a single entity, not as the individual creatures, for purposes of dealing or receiving damage. So the swarm, in your case deals an automatic 1d6 damage, as a single damage instance. That damage is reduced by damage reduction.
It does not matter if the damage reduction would be sufficient to blank all damage of a single individual creature in the swarm.
(I have no good explanation for a narrative as to how that works, and therefore might be inclined to rule differently in my home game, and say that if the reduction is sufficient to block all damage from a specimen in the swarm it will block all damage, but the rules do not have support for that).
However, there is this additional rule text you quote:
Damage reduction sufficient to reduce a swarm attack’s damage to 0, being incorporeal, or other Special Abilities usually give a creature immunity (or at least resistance) to damage from a swarm.
One way to read this is that if the damage reduction is large enough to reduce any one of the swarm's possible damage outcomes to 0, then the creature will be immune (or at least resistant) to the swarm's damage. So a creature with DR 1 would be immune to swarm of 1-5 HD, but not to one of 6-10 HD, because 1 is one of the smaller HD swarm's possible damage outcomes, but not of the larger HD swarm's.
In effect, this reading will achieve a very similar outcome as if individual creature damage counted: any amount damage reduction would blank damage from a swarm of creatures that can only deal one point, like in your example. This is because the swarm might only deal 1 point, not the creature does only deal one point, but who cares?
I think it is not entirely airtight an argument. The passage also could mean instead that you need a DR needing high enough to blank all of the swarms possible damage outcomes, and might still not be superfluous, as this is not normal damage, it is automatic damage, which is not otherwise defined, and the passage might aim to clarify that DR would still work. So, which of the two to apply may still be up to DM adjudication; I would go with the first, as it nicely solves the narrative issue without going of the rules text.