In the eyes of Putin and the Siloviki, Chechen nationalism was a concrete threat to Russia and the Jihadis were an abstract threat and a useful tool.

The nationalists defeated the Russian Army in the First Chechen War achieving de facto independence, and had legitimacy in the eyes of the international world. The Siloviki were convinced of foreign meddling in the conflict, and viewed the issue in the context of a greater process of the fracture and disintegration of the Russian Federation.

You let one tribe go free and soon all the others will want independence. As go the Chechens, so go the Ingush…the Dagestanis…the Karachays…etc. Then goes the North Caucasus, and much of Russia’s access to the Caspian.

To Putin and company it is about keeping and maintaining control. The Jihadis are the cost of defeating the Chechen nationalist movement and maintaining control. The loss of innocent life - both ethnic Russian and Caucasian, does not factor into their decision making.