So are there any words that differentiate foreign bodies in the human body that between neutral, beneficial, and disadvantageous foreign bodies.
In addition to Edwin's post (where all the terms can be made into nouns quite easily if that's what is needed), I would also like to add:
"parasite" (a foreign body which feeds off of and/or relies on its host for survival, to the host's body's detriment: leeches, ticks, intestinal worms, a foetus...)
"Symbiont" (like a parasite, only it helps its host: our gut flora that help us digest foods, for example, or a clown fish living in a sea anemone.)
(I can't recall if there is a third option where the effect to the host is neutral. Grade 9/10 science was a long time ago. Though note: these all describe relationships where an organism depends on the host, be that host a human body or otherwise).
pathological has the sense 'relating to disease' and this sense is the default one in 'pathological organisms'.
pathological: (2) Involving or caused by a physical or mental disease [ODO]
pathogenic also means 'causing disease'
... infectious disease that can be spread by any pathological organism transmitted by and to humans ... [CourseHero]
benign means 'not harmful' in this context.
1a Having little or no detrimental effect; harmless
b Of no danger to health; not malignant or disease-causing [AHD]
beneficial is commonly used for foreign organisms that actually benefit the host.
Bacteria are the most abundant form of life on the planet. They are found in most every environment, from Antarctic ice, to boiling hydrothermal vents, to inside your stomach. Most of these do not hurt us. Actually, many of these organisms are very important to our survival. [ASU: Ask a biologist]