That's just the protomolecule, which itself is a tool of the Builders. Through the projection of the Investigator (a troubleshooting sub-program of the protomolecule) fucking with Holden's brain, it is explained that it is merely a tool, a particularly clever one capable of a lot of agency for a blob of grey (or rather blue) goo, but merely a tool with the purpose of recycling biological material into gates that was limited in other regards. It could not by itself decide to fuckoff and rebuild the Builder civilization, all it does after the gate is built is as a consequence of the directive in its programing saying that it needs to successfully restablish contact with the creators once the gate is operational. But all its calls to report
mission complete fail to get an expected (or any) response, so what agency it had made it try to troubleshoot the issue and try to establish what the root cause is and if it has to keep trying to make contact, hence why its chapters/interludes/whatever start with "it reaches out it reaches out":
Cibola Burn said:
“—it reaches out it reaches out it reaches out it reaches out— One hundred and thirteen times a second, nothing answers and it reaches out. It is not conscious, though parts of it are. There are structures within it that were once separate organisms; aboriginal, evolved, and complex. It is designed to improvise, to use what is there and then move on. Good enough is good enough, and so the artifacts are ignored or adapted. The conscious parts try to make sense of the reaching out. Try to interpret it.”
This is why through the investigator it tries to get Holden to find out what happened with its masters/creators, it improvises to fullfill the directive and fucking with Holden's brain to communicate with him is one such improvised action. It needs to verify if there is anyone left to answer and if it need to keep trying or essentially die (and after all it does tell Holden to basically kill it after it gets its answer, since it no longer has any directives to fullfill nor purpose).
Supposedly it was not meant to consume more complex ecosystems than purely microbial ones, hence why Eros was such a freakshow, but there's a lot of ambiguity here if the builders actually would give a shit if they sent it towards planets with intelligent life. Per the quote above, it's designed to improvise and use what is there. Whether the creators lacked imagination or just didn't care for possible sentient life getting in the way and getting gobbled up, ripcages crawling along the floor propelled by one skeletal arm dragging it forward and all that, is left ambigous in the series.
But in any case it's not the Builders as such that did the biomass hijacking into their hivemind, the gatebuilder goo they made the hijacking and primarily to build things with it. For them gate building was a process like say hunting animals to skin them is for us, resource extraction, and instead of a rifle and a skinning knife (and whatever other tools are needed for that kind of thing, I'm no hunter) they had the protomolecule to handle the whole thing, only they hunted whole ecosystems.