We're not doing it for 6 fish. 6 fish are all we have left this year, whereas it used to be several thousand fish. (Edit: I should say that we have only found 6 in the annual survey. There might be hundreds or thousands in total; I don't know the exact relationship between the sample and the overall population,a nd I'm not sure anyone has an exact number.) We only found out that there are only 6 left about 3 weeks ago. The amount of water allocated doesn't immediately get adjusted to reflect the fish population.
Also, it's not meaningful to look at the water allocation on a water-per-individual-fish basis. What's the point of diverting this water at all? To ensure that there's a flow on a particular river tributary to allow fish to swim upstream to spawn. How much does it need? That's very much a function of the geography of the river - its length, composition, elevation and so on, and the length of time that you need to ensure water flow for successful spawning. Any number of fish, whether it's 6 or 6 million, need to ave water flowing along the whole length of the river if they're to swim upstream to spawn.
So look, if these are in fact the last 6 delta smelt in existence that's sad but I'm not going to lose sleep if they die. Maybe we can put their DNA in cryogenic storage and reintroduce it someday or something. But if we decide to cut off that water, then we have to accept that probably nothing spawns in this tributary of the Sacramento river at all and that whole branch of the river dies, potentially affecting many other species.
If it helps, think of the river like part of the interstate highway system. You can try to save money on maintenance or so, but if a major bridge goes out then whole large sections of freeway become useless.