Any magical attack against a clay golem that deals acid damage heals 1 point of damage for every 3 points of damage it would otherwise deal
Absorption replaces actual damage.
I think you're confused about what SR is. SR is simply a chance to negate the effects of a spell entirely if the caster fails a caster level check vs your SR.
The extraordinary ability that grants a clay golem healing from acid is something different altogether. It has nothing to do with SR.
Therefore, yes, the golem would be healed.