Upvote:2
"Sepoy" was a name given to a retributed soldier engaged by trade companies in India. As a whole, it included Muslim as well as Hindu soldiers. The mutiny was mainly caused by Hindu soldiers but Muslim soldiers participated as well.
In the 1860s and 1870s, other rebellion events triggered suspicion by the British about Muslim subjects that were geographically and culturally close to Afghanistan and Central Asia, where the British had difficulty to go and become sovereign. This explains the treatment of the Muslims in India as a problematic minority. This has not a lot to do with the Sepoy Mutiny.
But not that besides the current of "theorizing the race" that spread in the end of the 19th century (it was about measuring heads to measure intelligence, theories about the genetics of crime (see Zola), etc...) and address nearly every specific population as having specific features; besides that, the Muslims were left in the administration and military works and had their place there, like the Punjabis.