However, I would also point out that Xinjiang has never been a tranquil region since it was most recently incorporated into Chinese territory in the Qing Dynasty. The Qing fought quite a few battles with Uighur tribes, and this kind of history has a lasting and reverberating impact.
I agree with the rest of your post and the general meaning of it, but not quit with this part.
First Uyghurs are not nomads, they are settled farmers in village or traders and craftmen in the city. They therefor do not live in tribes.
Second, The Qing did not fight more or severer battles with Uyghurs than any other group of people in other part of China. I emphasize this to say that Uyghur issue is not really an issue to the government back then.
The most significent war that Qing fought in Xinjing was actually with the Dzungars, an Oriat Mongol tribe in the northen part of Xinjiang which is mostly settled by various Mongol tribes instead of Uyghurs who concentrated in the southern part of Xinjiang and were relatively peaceful with the Qing government. After the campain against the Dzungars, northern Xinjing was repopulated by state orgnized imigrants of Han, Hui, Manchu, loyal Mongols and Uyghurs. I remember reading a source saying that there was a quota or ratio of 2:9 (Han/Manchu : Uyghur). The reason was that the Han and Manchus are settled soldiers, while Uyghurs were farmers as they were in their southern home. The ratio is to make sure the garrison is supported by the local populations.
The latest war in late Qing was in the 1870s Muslim rebelling in many western provinces including Xinjing. But the main rebels were Hui (Chinese Muslim), not Uyghurs.
The last part of the campain was between Qing and a foreigner Yaqub Beg from morden day Tajikstan with Russian backing. It ended in 1878. BTW, I can not find his ethnic background, so I would not blame Uyghurs for his act.
All the significant fights between the Uyghur population and the Qing in its last days had Russia (1900s and onwards) and Soviet Union and Turkey (1930s and on wards) shadows. They were never Qing or Chinese republics initiations.
From this you can see that for most part of the time till the end of 19th centry, Uyghurs were not making any more troubles than other Chinese populations.