Dear Sridham das; 
Please accept my humble obeisances. All glories to Srila Prabhupada.

Are those the cows at Jaganatha Mandir? 

Cowpox:
Are there two questions you need to ask?
1. What should we do to help the cows?
2. Should we drink their milk to develop immunity to smallpox? 

Treatment for cow pox:
Have not treated this problem but in the past in America in the past they use to treat with dock/elderberry salve and dowse cows with garlic. A disinfectant is needed. If you have neem oil it could be used by massaging it in to similar effect or you can do the following.

Remove food from infected animals for a 24 hour period. At the end of that period they should be fed a diet that is made up solely of fresh cut forage. No grains, cakes or non-green foods should be fed.

At the following morning milking the cows should be fed 1 bulb of garlic (Allium sativum, ) that as been crushed. 

The following salve should be made and massaged into the infected areas.

Part one: Take equal parts beeswax and nut fat place under low heat, stir until the whole mass liquefies and becomes uniform.

Part two: In a small tin put some olive oil and 8 cloves of garlic, tie a cloth around it and put in to a pan of water and boil for two hours. 

Part three:
Lower the heat and mix in the ingredients from part one then remove from the heat. The salve should be applied warm to the infected areas.

Disease prevention.
Following are some guidelines based on Ayurveda:
Cleanliness, no over-indulgence or under-indulgence, freedom from stress. The best way to avoid contracting any disease is proper hygiene, adequate rest, and a healthy diet including herbs, avoiding sugar, artificial ingredients and preservatives. Sugar weakens the immune system, increases the incidences of infection and the body's ability to protect itself from disease. Just 100mg of sugar (8oz of soda contains an average of 29 grams [2900mg]) reduces immune function by 50% in one hour. 

Building up the body's natural immunity and taking responsibility for any illness that may invade the body is more beneficial than being injected with foreign proteins and toxic substances. If the immune system is undermined and not allowed to handle disease in its own way, its ability to protect the body throughout life is lessened. Disease tissue is not caused by germs. It attracts germs. Germs help decompose dying cells, so they may be eliminated by the body. Disease is the cleansing effort of the body, to rid itself of toxins and waste material. 

April 18 1977 Bombay
Dr. Sharma: Even the smallpox vaccination that was discovered by Edgar Jenner in 1796, it was really from the cow pox serum they discovered. The first vaccination he used on his own son. (indistinct) People who were living with the cows, they were not affected by smallpox, though the people did not have a cow in the house, they were affected the most. So it protects from cow pox, small pox.

Prabhupäda: Oh, yes. Cow protection protects us from so many infectious diseases.

Dr. Sharma: Even the cows, they have habit to take the leaves along the banks of the river. The iodine content of the grass is so high. It has got iodine in that. So if you smear cow dung on the floor... It is said it is an obnoxious thing. There is tincture of iodine sold in the shops (indistinct). It is most unfortunate that we do not appreciate, the nature itself is giving us aids.

Prabhupäda: We take it seriously because Kåñëa says. Kåñëa is our authority. He says, kåñi-go-rakñya. Go-rakñya: "You must give protection to the cows." This is authority.

Dr. Sharma: And the proper facility appears in the rights and democratic (indistinct). But we have a right to live on this planet. Why should we (indistinct) the right of another man?

Prabhupäda: They are... They are... They are described in the Bhägavata, päpinaù. Those who are killing other animals for maintaining his own body, they are very, very sinful. Very, very sinful. Therefore untouchable. According to Vedic civilization, the animal-killers, mlecchas, they are untouchable. They are so sinful.

June 10 1975 Honolulu
Prabhupäda: Yes, does it mean smallpox is stopped all over the world? 
Harikeça: It's very much cut down. There's hardly any smallpox...
Prabhupäda: Very much cut down, but it's very much increasing in another side.
Siddha-svarüpa: No, no, they have smallpox.
Harikeça: In America there's no smallpox. So that means here...
Prabhupäda: That is all right. It is due to poverty, uncleanliness. So that is known to everyone. The smallpox takes place amongst the poorer class, unclean class. In India also, that is there. No gentleman's house, there is smallpox. Only these lower class, unclean.
Siddha-svarüpa: Where there's no facility for sanitation...
Prabhupäda: If you remain unclean, all diseases will come. Where is the cure?
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ys, Rohita dasa