Firstly, Stalin did not establish the Zhenotdel, they were creations of the Bolsheviks operating under the aegis of Lenin. The mostly male Bolshevik leadership had given little thought to the woman question prior to 1917, thus female Bolsheviks such as Aleksandra Kollontai and other like-minded individuals had something of a carte blanche to create the new regime's gender policies. This initially was congruent with the precepts of the Bolsheviks to create a new socialist man (and by extension, woman), but the Zhenotdel were always at the mercy of the central state's largesse. Few within the corridors of Soviet power in the 1920s saw the urgent need for women's rights and they often harbored quite sexist mentalities towards women, but Moscow tolerated the Zhenotdel because their activities seldom interfered with centralization and the functioning of the Party.

The Zhenotdel were further handicapped by the fact that a number of its leading members had sided against the Stalinist faction in the late 1920s. The archetype of the Zhenotdel activist, intellectual and urbane, was also uncomfortably close to the type of Party member that supported Trotsky. Thus as Stalin cemented his dictatorship, the state declared that the Zhenotdel had accomplished their purpose by uplifting women within the Soviet core, although they remained in action in Central Asia, and they were thus no longer necessary. While the early Bolshevik state begrudgingly accepted the Zhenotdel, the Stalinist state saw no need for it.

Source

Wood, Elizabeth A.The Baba and the Comrade Gender and Politics in Revolutionary Russia. Bloomington: Indiana University Press, 1997.