In Jainism this exact doubt is accepted and answered very clearly: “Yes, in saṁsār some level of himsā to very small beings is almost unavoidable – yet moksha is still fully possible.”

Very simple way to see it:

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1. Two kinds of hiṁsā

Jain āchāryas clearly distinguish:

1. Saṅkalpi hiṁsā – intentional, desire‑based violence

- Done with anger, pride, deceit, greed, attachment, hatred. - Example: killing insects for fun, cutting trees carelessly, eating non‑veg, doing business that harms many beings. - This brings heavy karmas and blocks moksha.

1. Ārambhi / unavoidable hiṁsā – linked with basic survival

- Walking, breathing, drinking water, eating even pratyek‑vanaspati (single‑soul plants) – all crush innumerable tiny jīvas and nigodas. - Scriptures call this anivārya hiṁsā (unavoidable violence). - If there is no intention to harm, and you minimize it sincerely, the karmic bondage is much lighter.

So: microscopic life is harmed, but if it is unintentional, minimized and without passions, it does not stop moksha.

You can read basic tattva explanation here

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2. How monks show that moksha is possible

Jain monks and nuns are the practical proof of this principle.

They take very strong steps to reduce even microscopic harm:

• Filter water, eat limited pure food, fixed time, no night‑eating
• Sweep the path softly before walking
• Avoid vehicles, farming, business, factories, etc.
• Live with extreme care in every movement (samiti, gupti)

Still, even for them, some subtle himsā happens (breathing, existing). Yet Jain scriptures say:

• If all intentional hiṁsā and all passions stop, and
• Asrava (inflow of karma) is mostly stopped, and past karmas are burnt by austerities,

then the soul can and does attain keval‑jñān and finally moksha.

So complete absence of any contact with tiny jīvas is not the requirement. The requirement is absence of rāg–dveṣ (attachment–aversion) and maximum possible minimization of harm.

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3. Why “microscopic harm” does not make moksha impossible

In brief:

1. Law is about bhāva (inner state), not just dravya (outer act).

- Same outer act can bind heavy or light karma depending on intention.

1. Universe is beginningless and endless, filled with infinite jīvas.

- Total non‑contact with all jīvas is impossible while embodied. - Therefore, shāstras speak of “yathā‑śakti ahimsa” – non‑violence to the best of one’s capacity.

1. Karmic bondage is graded.

- Killing a five‑sensed being with cruelty ≫≫ crushing countless one‑sensed micro‑jīvas unintentionally while breathing. - Hence focus is on completely giving up gross and intentional hiṁsā first, then refining subtler and subtler levels.

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4. Practical takeaway

For shravaks/shravikās (lay people):

• Avoid intentional himsā as much as possible (especially to 2–5 sensed beings).
• Follow vegetarian/vegan ahimsak diet, careful profession, day‑time eating, filters, etc.
• Do pratikraman for inevitable harm.

For munis/āryikās:

• Go much further – life of total renunciation and vigilance.
• They can reach the higher guṇasthānas and finally moksha.

Thus, in Jain dharma:

• Unavoidable, minimized microscopic harm does occur.
• It does not block moksha, if:

- All deliberate violence is abandoned, - Passions are destroyed, - Right faith, right knowledge, right conduct are perfected.

So moksha is not only “theoretically” possible; it is the central certainty of Jain philosophy, achieved by countless souls (siddhas), even though microscopic life was always present in the universe.