This game series takes place in an Alternate Universe in which Soviet Union (later Russia) and People's Republic of China had never reconcile after Sino-Soviet split in the 60s.
Which is apparent by looking at Lian Xing's assignments in Soviet-occupied Afghanistan, namely assassinating Soviet's snipers and documenting a map portraying Gregorov's troops. While her destroying Soviet munition cache to create a big explosion is to distract Soviet patrols so Gabe's convoy could enter the city as a payback for Gabe saving her life, her other tasks are given by MSS. Shi Hao belonged to Manchu ethnic, he wanted Syphon Filter virus as a weapon to wage war against both China and Russia, partially fueled by his past bitterness as a minority in a Han-dominated province, and partially to bring down communism.
Why else would he allied himself with a shady organization that doesn't even have an official acknowledgement from POTUS to obtain the virus?