Empathy for Deckard
It's the obvious explanation, after all. That doesn't guarantee its truth, but it does mean we should consider it first, and only discard it if we have good reason.
Here are some facts to consider:
- Gaff knows that Deckard has feelings for Rachael
We don't get much Deckard+Gaff time, so we don't see Deckard tell Gaff about his feelings (and I doubt he would), and so we must reach this conclusion by implication.
We know that Gaff tracks Rachel to Deckard's apartment.1 Once he realized Rachel was hiding in Deckard's home, an obvious question would have presented itself: why would a professional killer of Replicants be harboring a fugitive Replicant he's under direct orders to kill (and who happens to be a best-in-class simulation of a beautiful woman)?
The genre of hard-boiled detective fiction overwhelmingly presents one reason for such an arrangement: because the detective has fallen in love with the beautiful woman he's supposed to be investigating. And, as a rule, characters in the genre are very aware of that danger (i.e. it's not just meta-knowledge available only to the real-world audience).
- Deckard has earned Gaff's respect
Gaff does not seem to care for Deckard very much at the beginning of the film. But in the moments after Roy Batty dies, Gaff appears and says: "You've done a man's job, sir!" I am quite certain that Deckard is necessarily human, and so the significance of this statement is just that it is well-earned praise.
There is also credible reason to believe that Gaff's use of language is a signal of his improved opinion of Deckard: at the beginning, Gaff literally refuses to speak to Deckard in English, but at the end he does, to praise and empathize.
- Gaff knows that Rachel has an expiration date
Nexus 6 models have a four-year lifespan. That means "the Rachel problem" will eventually resolve itself. Gaff knows this because he is present when Bryant shares this information with Deckard.
He proves that he knows it by his other statement to Deckard at the end: "It's too bad she won't live." Importantly, he doesn't say:
- It's too bad you have to kill her
- It's too bad I'll have to kill her
- It's too bad blade runners will pursue her until one of them succeeds
He said precisely what he meant.
- Gaff believes Rachel is not dangerous
Rachel has not attempted to hurt any humans, unlike the other six Nexus 6 Replicants who are part of this incident. (I am including two that we never meet because they are killed by an electrical field trying to infiltrate Tyrell's HQ, as related by Bryant during the initial briefing.)
Importantly, Rachel does kill a Replicant: she fatally shoots Replicant Leon, saving human Deckard's life. This happens after she learns that she is herself a Replicant. She is a Replicant, but she still identifies with humans.
Gaff takes a calculated risk when he decides to spare Rachel's life. He does it for the sake of a colleague he has come to respect, a man whose judgement about Replicants has proven very reliable, a man who has just barely survived extraordinary dangers doing a job that might well have fallen to Gaff. And he knows that this gift is both a blessing and a curse, that Rachel will expire before too long and break Deckard's heart, that Deckard also knows this and still chooses it.
Gaff does it out of empathy. Which is only fitting.
1 The proof that Gaff tracks Rachael to Deckard's apartment is the origami unicorn he leaves at Deckard's doorstep. I'm not sure if that detail is in every version of the film; I only have access to the Director's Cut, and it's my understanding this might be a late addition intended by the director to bolster his attempt to ret-con Deckard into being a Replicant. I think my interpretation still works without this detail, because Gaff knows that the only reason Rachel would still be alive is that Deckard has chosen to disobey orders and not kill her. Since he hasn't reported her dead or turned in the body, Gaff presumes she is alive.