GSN 1612091751:
B-But... What if we don't WANT to be cyborgs?
You can always just stand around and say "no thanks". Then they will 'find' another parasite on you and try to determine what part of your brain is making you decline such wondrous upgrades to your poor, weak, fleshy shell. ;)
But seriously, you can indeed decline the upgrades. It doesn't give you anything to replace it, but it may make them suspicious of you in the future. Fortunately, the Inquisition is more of a concern, what with their Naughty List putting the Adeptus high up near the top [and this fleet in particular], so you're a relatively small and boring fish right now.