Is Atakhan's "kill a defender" considered an ability for purposes of Ruin Runner?

Yes, but it doesn't help Ruin Runner — Atakhan's kill effect is an ability, yet it doesn't "choose" or target Ruin Runner, so the protection never applies.

Atakhan's "When I attack, the defender must kill one of their units here" is a triggered ability (Rule 383), and Ruin Runner's "I can't be chosen by enemy spells and abilities" (Rule 756–757) would block it if it targeted. But it doesn't — the defending player makes the choice of which unit to kill during resolution (Rule 355.10.e: "Each player kills a unit they control" does not target). So if Ruin Runner is the only unit there, its controller is forced to kill it (FAQ #9598, matching the Cull the Weak ruling, FAQ #8681).