You are raising a very sensible and logical doubt. Let’s separate a few points one by one, from a Jain-dharma perspective.

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1. Menstruation in Jainism

• Menstruation is a natural bodily process, not a sin, not a “low” condition of the soul.
• What is called ashaucha (ritual non‑purity) applies to all active bodily discharges: blood, semen, urine, stool, mucus, etc.
• During such discharges, touching idols, scriptures, or doing certain temple rituals is avoided mainly for:

- Ahimsa: these fluids contain countless tiny forms of life. - Hygiene & respect: they are considered unclean for a place meant to represent the highest purity.

So the restriction is ritual and practical, not a judgment on the woman’s spiritual worth. (You can read more here )

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2. But milk is also a bodily secretion and has microorganisms – why is it used?

You are right:

• Milk is a bodily secretion of an animal, and
• It does contain microorganisms.

So why is it used in abhishek (ritual pouring on idols) and sometimes even to “clean” the idol?

a) Milk is not used as a disinfectant

In Jain achar, milk is not used because it is germ‑free. It is used as a puja-dravya (offering substance), symbolizing:

• Respect and devotion to the Jina
• Softness, nourishment, and śuddhi (purity in a ritual sense, not a laboratory sense)

The actual cleaning of the temple (removing dirt, dust, etc.) is done with:

• Water, cloth, sweeping, mopping, etc.

Milk abhishek is a religious offering, not a hygienic cleaning agent.

b) Why is milk considered acceptable but not menstrual blood?

Jain dharma accepts a graded approach to ahimsa:

• We cannot live without interacting with microorganisms at all.
• So the scriptures allow certain kinds of unavoidable or lesser himsa for grihasthas (householders), while still asking them to reduce it as much as possible.

On this basis, traditional achar says:

• Direct bodily excretions (human blood, urine, stool, nasal mucus, etc.) are ashuddha for worship and must not touch idols or scriptures.
• Certain external dravyas, like filtered water, certain types of milk, etc., are allowed as puja substances, even though they also contain microscopic life, because:

- They are not coming directly from the worshipper’s body at that moment. - They have been culturally and scripturally classified as acceptable vyavahārik (conventional) substances for worship. - The ideal of zero himsa is approached step by step within what is practically possible for laypeople.

So, from the traditional standpoint:

• Menstrual blood = person’s own current bodily discharge, considered ashoucha, so that person avoids certain acts for a few days.
• Milk = external substance, scripturally permitted, used in limited quantity as an offering.

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3. What about microorganisms in milk?

Jain texts and acharyas clearly accept that all food and liquids contain tiny living beings. The rule is therefore:

• Don’t try to eliminate every single micro‑organism (impossible in samsar).
• Do your best to:

- Avoid unnecessary and gross forms of himsa. - Follow the graded vows suitable for your stage (monk vs householder). - Use only those substances that are traditionally allowed for puja and food, in careful ways (filtering, avoiding stale items, etc.).

That is why:

• Many Digambar munis today avoid milk altogether, as an extra step in ahimsa.
• But householders are still generally permitted to use milk, especially in very small amounts for puja.

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4. Is there a contradiction or hypocrisy?

If we look at it like modern science only (“everything has germs”), it can feel contradictory.

From the Jain point of view, it is based on two key ideas:

1. Gradation of rules

- Direct fresh bodily discharge on the temple/idol = strictly avoided. - Using small quantities of certain allowed dravyas (like milk) = permitted, though even this is now questioned by many Jains who are moving toward more ahimsa‑sensitive practices (e.g. only water abhishek).

1. Symbolic / devotional use

- Milk in abhishek is more about bhav (inner devotion) and traditional symbolism than about actual sterilization. - Temple purity is kept mainly through cleanliness, filtering, and careful behavior, not through the chemical power of milk.

So, in simple terms:

• Menstruation is not a sin; it is a temporary state where direct bodily discharge leads to certain ritual restrictions.
• Milk is also a secretion and has microorganisms, but it is scripturally permitted as a symbolic, external offering in limited quantity.
• Many thoughtful Jains today are re‑examining dairy use in light of modern himsa in the dairy industry; moving toward more water‑based or simplified puja is fully in line with Jain principles of ahimsa and aparigraha.

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If you personally feel uncomfortable with milk abhishek because of himsa or logic, Jain dharma fully allows you to:

• Do only water abhishek, or
• Do only bhav‑puja (mental worship, mantra, meditation) without any liquid at all.

The core is always: purity of the soul and intention, more than the substance used.