There are a few sets of rules which specifically cover the mutiny including:
John Company (3rd Edition)
A Miniatures Game System for Warfare on the Sub-Continent 1750-1860
Chris Feree and Patrick R. Wilson
John Company is intended to cover all the campaigns of the Honourable East India Company from 1750 to 1860. The smallest unit is an Infantry Battalion, Cavalry Regiment or Artillery Battery and the rules recommend a player for each Brigade (or roughly 50 figure bases).
My first look at these rules can be found here.
The Devil's Wind
Rules for Wargaming Battles from the Indian Mutiny 1857-58
Overall these are a decent basic set of traditional style rules which will give a game in an evening. They include some automatic generation rules for the Mutineer forces but these are pretty basic. Despite the terminology and the inclusion of rules for various theatre specific units they don't manage to convey much of the "feel" of the period to me (maybe that's just me of course!). My first look at these rules can be found here and my first play here.
Wargames Rules for the Indian Mutiny
Based on Peter Berry's File Leader rules these fit the gap between a skirmish and a full battle set of rules.
I can't comment more on the rules as I have yet to play them.
The following are rules designed for other periods which can be used and have some relevance to the Mutiny:
Wargames Rules for Large Skirmishes in the Black Powder Era
These are a set of rules from the Too Fat Lardies for wargaming the actions of literary heroes, with swashbuckling advantures in the black powder age and fit in the gap between wargaming and role playing and allow the gamer to fight large scale skirmishes between 30 and 120 figures per side.
Modifications for the Mutiny - A Damnably Close Run Thing - are contained in the 2008 Christmas Special also available from the Too Fat Lardies.
Fire and Steel
Skirmish Wargames Rules 1700-1900
These are a generic set of skirmish rules for the period stated but do have stats and a scenario to cover the Mutiny.