Free-will within the Lifeweb might be seen as a curse more than a blessing.
Individual Symbiots could retain free-will through a variety of means. Weak infestation, unusually strong will, and extreme Wyrd energy might all allow for more free-will than one would expect in a Symbiot. However, such free-will within the Lifeweb might be seen as a curse more than a blessing. With the freedom comes distance and isolation from the Lifeweb; the Symbiot knows it is there and can taste it, but can't truly join with it. The experience would be similar to seeing Paradise, but being able to enter (at least to the Symbiot).
"Mindless killing machines" are created when a person becomes a Symbiot and truly joins the Lifeweb. His life, his essence, and/or soul leaves his body and becomes one with the flow of all other essences in the Web. Should the Symbiots need a worker/soldier/whatever, they infuse the body with the needed amount of essence (form the Lifeweb's pool) for the job. Of course, the Symbiots' definition of need doesn't just revolve around "infect all life"; all bodies are filled with essence at all times, and assigned specific roles. When not directed by superiors, warriors will hunt workers, and workers will defend against soldiers; these inter-Symbiot wars seem like a pale mockery of balanced nature to outside observers, but the Symbiots disagree.
Big monsters (i.e. any non microboes) are used when trying to break through uninfected defenses, or crush uninfected resistance. Attempts to leave the Symbiot systems require special ships to break through to the Jumpgates; potentially harmful weapons or wyrd powers must be neutralized quickly and efficiently; planetary infection might be better carried out by an initial infection of planet leaders. Microbes on the other hand are ideal when time and enemy defenses are not a factor. Symbiot spores could be designed to survive space travel and planetary entry (maybe with some sort of tech or -thick- protective layering), and infect a planet over the course of decades or centuries; Symbiot spores might be released over a planet's arable land, further infecting all who eat any of the infected food; micro-organisms could also be used directly against enemy forces, turning surviver into Symbiot plague carriers.
When developing Symbiot technology/methodology, make it weird, alien, and -very- scary. They aren't demons, but they should -seem- like it.
We know they have strange environmental weapons like lightning and hail storm guns. Perhaps the Symbiots have perfected ideal terraformation, but seek to infect all currently existing life before expanding to uninhabitable worlds; the infection of existing life is quicker than full terraformation, and removes a potential later threat. Imagine an enemy that could control your entire planet's weather and geological activity. Refuse to submit to the Lifeweb, and they create a drought over your cropland; eat their food and join the Web. Enemy cities are leveled by earthquakes, rapidly grown volcanoes, tornados, floods, and more. I'd assume that such large-scale projects require numerous Symbiots (to focus the Lifeweb on an area), and certain special pieces of Symbiot tech.
As far as bio-tech goes, I'd say that it's all "born and bred" instead of "harvested and ripped". Much like we make multiple parts for a specific item, the Symbiots probably grow various small organisms to fulfill certain task and combine them in various ways (symbiotically of course) to form one machine. These miniature Symbiots are not intentionally built or designed, they just "know" what form to evolve into based on "instructions" from the Lifeweb. It's not so much a science as it an instinct. Free willed Symbiots can subconciously request specific items or parts, provided that available Symbiots exist to breed or be mutated into the needed parts.
A cool source of ideas for Symbiots is Warhammer 40,000's "Codex: Tyranids". Lots of hive mind grwon bio-tech monstrosities.
I seriously doubt that there is a connection between the Light, Dark, and the Lifeweb. The Light is good, the Dark is evil, and the Lifeweb is life. Not just the happy butterflies and hummingbirds, but the scavenging vulture and the parasitic larvae. The Lifeweb is beautiful and hideous at the same time, and more alive than people truly want. Joining the Lifeweb is to trade any reason or logic in exchange for instinct and drive. That being said, there is also more to the Lifeweb than mere instinct and drive; the Lifeweb guides those who make it up, and strives to add more to it for the sake of its own survival and propagation. Psionics and Theurgy function so well against the Symbiots because they function on the same level as the Lifeweb. When a pyrokinetic attacks a Symbiot, not only does his Wyrd energy burn the body, but it interferes with the Lifeweb through its connection to said Symbiot. A similar thing with Theurgy applies in that the Wyrd energy focused by faith interferes with the Lifeweb as well (perhaps more so due to possible external entity involvement). Perhaps the Lifeweb is composed not of souls, but of Wyrd, all the Wyrd of all the life it has absorbed into itself.