By the mid 19th century, the dangers of cholera were well known, especially in the context of long sea voyages . Considering the open living spaces and proximity in which the ship’s inhabitants lived, an outbreak of cholera could spread across the crew and passengers rapidly. Indian emigrant ships in particular were said to need more medical attention, as surgeons like Pearse found Indian coolies to be less resilient than coolies of other races, like the ‘Chinee’.

While no cure for cholera was available at the time, numerous measures were taken to mitigate its spread.

On ships that had cholera outbreaks, the bedding of the victims were destroyed. The deck was also cleaned and scraped with holystones and washed with Burnett’s fluid (a composite disinfectant). Furthermore, ships are fumigated with chlorine and heated sand half an inch thick was layered on deck. Charcoal fires were also lit on the poop deck to clear the air. This helped create clean living quarters that not only reduced the chances of a cholera outbreak, but also helped create an atmosphere conducive for recovery.

Furthermore, morale boosting activities were employed to encourage emigrants to reboard a ship with a cholera outbreak. To cheer up the passengers, the ship provided better food, as well as special items such as beer, while they were marooned (and the ship was being cleaned).

Aware of the importance of eliminating cholera outbreaks, companies also shouldered the cost of the treatment for cholera. This was not the case with all diseases, such as sexually transmitted disease (where the indentured labourer or the crew member would have been complicit as well). For example, John Sullivan, an able bodied seaman on the Clarence (on a different voyage that commenced in 1863), was not docked any wages when his account was being settled. This would have been determined by the surgeon of the ship, who in this case was  Charles Turner, the surgeon on our voyage of the Clarence as well. Had he been afflicted with some other ailment, such as venereal disease, Sullivan would have had his wages used to cover the costs of treatment. This goes to show the measures taken by shipping companies of the time to assuage the fears of sailors, who might have otherwise been discouraged from sailing due to cholera.
Sources:

Sarup, Leela Gujadhur. "Volume 6." Colonial Emigration, 19th-20th Centuries: Proceedings. Kolkata: Aldrich International, 2009 N. p. Print.
Reading the Handwriting | More Than a List of Crew "Reading the Handwriting |.. More Than a List of Crew Memorial University of Newfoundland, nd Web 12 Nov. 2015.
Lubbock, Basil. Coolie Oil Ships and Sailors. Glasgow: Brown, Son & Ferguson, 1935. Print.
Haines, Robin F. Doctors at Sea: Emigrant Voyages to Colonial Australia. New York, NY: Palgrave Macmillan, 2005. Print.