Lets looks at major military powers in the globe
US, China and Russia
Out of the above 3 which one has the greatest possibility of being an ally of Muslims?
As a fragmented, diverse and geographically dispersed population, Muslims need alliance with at least one power, to get out of their weakness, don't you think? Who will supply us with advanced military tech if we are not allied with at least one of the 3 major powers?
I am well aware of Chinese history with Muslims, but this was a long time ago and have no significance at present time. Even if you consider history, the West, Russia, India, these countries had much more serious conflicts with Muslims throughout history.
Currently the only issue China has is with Uighur ethnicity it seems, mainly because Uighurs probably feel that they do not have a home of their own, unlike Kazakh, Kyrgyz or Tajik, all of whom have a state of their own. But Uighurs are not the only ethnic group without a home state, Hui is more numerous than Uighurs I believe. The Qing experience you mentioned were mainly about these Hui Muslim rebellions, trying to make their own states, which were brutally crushed. But look at the Hui's today, they are the most integrated and loyal Chinese Muslim citizens.
I have been to Xinjiang and traveled there extensively. I know how Uighurs live there. Things may have been not so good in the past, but they are not being treated like the Rohingya in Myanmar for example. Everyone I talked to is hopeful about the future. China is a growing economy and emerging super power and they know they will have much more opportunity staying with this great country. Trade with former Soviet Central Asia and Russia has already opened a lot of opportunities among Uighurs in Urumqi and other towns. Only fools think of separating from China, which is not possible anyways, as China will not let it happen.
So the best advice we can give Uighurs is to build bridges with Han Chinese, for their own sake and for the sake of wider Muslim world, who need China more than they need us. It is also their duty to inform the authorities of any terrorist backers among the Uighur diaspora living in the West and Turkey. My suspicion is on Turkey, as it will not be hard to find some idiot Uighur living in Turkey to supervise a terror campaign, making him think that he is trying to liberate his people. In the West someone like that will easily get caught through surveillance. This would be a really cheap way to spread fear among Han Chinese, make them suspicious of Uighurs, ruin Han-Uighur relations and thus break down social harmony and destabilize Chinese society. As China becomes powerful, this would be one way for China's enemies and competitors to bring down China one notch, just like Osama Bin Laden sought to bleed the US.