In fact, Safeguards don't mean to act against humans, do they ? They're made to eliminate hackers (broadly speaking, people who don't have a netgenes terminal, and especially silicon creatures). Then when a Safeguard is downloaded into the "basic reality", it kills unregistered people, who are considered as a threat for the Netsphere.

The Rule Bureau wants to stop Safeguards, but they can't. All they can do is creating "temporary Safeguards" (like Dhomo). That's why Dhomo protects humans : his brain doesn't contains the "kill people without netgenes terminal" directive.

As for Sanakan, she's a proper "Safeguard from the net" until volume06 or so. Her mission is to slay "hackers", that is. But when Killy destroys Sanakan, a backup of her is still stored somewhere. Of course, the Rule Bureau has removed the "kill unregistered humans" directive from Sanakan's backup. So when she's reloaded in volume10, she's "humans friendly".
Concerning the Sanakan that helps Level9 Cibo, I think she's the "original", organic Sanakan. As she's a Rule Bureau Agent, her mind is saved somewhere, so as to make "copies", just in case... But in fact, this save was used to make a Safeguard.

And what about Killy ? Well, he seems to have worked with humans killing Safeguards once. Perhaps at a time he was badly damaged, even desactivated. Then, the Rule Bureau succeeded in "reseting" Killy, to make a humans helping agent of him.
As Iko says, Killy doesn't have a registered number. That must be why Safeguards try to kill him (except for Sanakan in volume03, because she knows him).

I think ur explaination of Sananka is quite right. However, it doesnt seem to me that Killy is the same as her. If u remember in vol. 4, the gover agent told cibo that Killy is a secret agent before the safegard system (even before the time of NOISE). Furthermore, the metrial that make up kILLY is completely different from safegard. It seems to me that Killy is the same guy that appear in BIOMEGA (they both have a similar gun). Or in other words, they are the same form (synthetic human).

By the way, did you noticed that in Noise (when Susono Musubi goes to find the two "cabled" children), a portrait of a missing child strongly looks like Killy ? Maybe it's purely coincidental ; after all, in Blame!, a few characters look like each other...

But still... what if Killy was kidnapped by the Order, so as to be a kind of experimental silicon creature thingy ? Later, he could have been "reset" and used by the Rule Bureau, couldn't he ?...