If I use Retreat on my Ekko, and chain Sacrifice on the same Ekko, does Retreat still give me the rune?

No, you will not receive the rune.

Ruling

According to RiftJudge FAQ #7774, if the unit targeted by Retreat is removed from the battlefield before Retreat resolves, the spell cannot return the unit to its owner's hand. Because the target is no longer present, the spell cannot complete its first instruction, and the subsequent instruction—channeling the rune—will not occur.

Sequence of Events

1. Cast Retreat: You play Retreat, targeting your Ekko. You place it on the chain. Retreat requires a valid target (the unit) to be played.
2. Chain Reaction: In response, you play the spell Sacrifice, choosing the same Ekko. The cost of the spell is paid at this time.
3. Closed State: The chain is now closed. The Sacrifice spell is on top of the chain, with Retreat beneath it.
4. Resolution (LIFO - Last-In, First-Out):
   • Sacrifice: Resolves first. Ekko leaves the board and enters the trash.
   • Retreat: As the next item on the chain, Retreat attempts to resolve. It looks for its target (Ekko) on the battlefield. Because the unit is no longer there, the instruction to return it to your hand fails. Per RiftJudge FAQ #7774, because the spell cannot return the owner's unit, it does not proceed to the instruction to channel the rune.

Note: I could not fully verify this ruling against the retrieved rules.