I would argue that the British Raj was a good thing for the muslims in sub-continent because by the time of Bahadur Shah Zafar in 1850s, the Mughals were at their weakest and their decline had become inevitable.
If the british had not taken control of the sub-continent, then the Hindu Marathas in western india and sikhs in punjab would have become dominant force all over sub-continent and Muslims would have been forced to live under their Hindu Raj. I think that would have been even more disastrous for the muslims than the white man's British raj?
The British raj filled that power vacuum at a crucial time in history, and allowed the muslims to regroup first under Sir Syed Ahmad khan's leadership, who worked for the educational upliftment of muslims in the late 1800s. And later the Quaid-e-Azam's muslim league fought to ensure that muslims have Pakistan and the hindu baniyas don't rule over the entire sub-continent