Oh, sure. Samurai were a severely outnumbered minority in Japan. Jurchen were a severely outnumbered minority in China, and so were Manchu.
The Qing army was 24 banners, of 60 000 Manchu, 60 000 Mongols and 60 000 Chinese, and Green Standard Army of 600 000 Chinese.
Out of the 60 000 Manchu soldiers of the 8 Banners, how many did Qing leave at home in Manchuria, and how many were deployed in China Proper? Inclusive of Beijing and vicinity?
Probably not too many. Last I checked, they relied a lot on Han officials to run the country thereafter.
But yea, he could probably stuff a lot of samurai in key positions in the Chinese administration to control the area. I doubt it'll be very effective in the long run though. If anything, he's recreating the same conditions that had plagued several Chinese dynasties in the past, giving local lords autonomous powers and setting a precedent of a country divided into many petty states (ironically the case for Sengoku Japan). If some got ideas and gained support from the locals (likely by assimilation into Chinese society)...