During my Deployment Phase I play Yoda.

My opponent plays Force Choke on Yoda for 1 damage and his Vader's reaction does another 1 damage on Yoda, destroying him.

In my hand I've Old Ben's Spirit. I won't be able to play this card on Yoda to save him, right?

Right. His action was to play Force Choke, and he uses Vader's ability as a reaction to Force Choke. Yoda will be dead before you get a chance to play Old Ben's Spirit on him.

Something like a Lightsaber Deflection would be able to save him, since that is an interrupt.

You could also sacrifice C-3PO or use Counter-Stroke to keep Yoda Alive. He would have 1 damage on him because Vader's Reaction would still happen but you could then apply Old Ben's Spirit to keep Yoda in play longer.