Who takes a stance against the Jews ...

For I, the L-rd, dwell in the midst of the Children of Israel (Num. 35:43)
Our Rabbis elucidated: When the Jews were exiled to Edom (Rome, the West), the Shechina (G-d's presence) went with them. This also occurs on the personal level within the soul of every Jew. When a person commits a sin and causes his soul to go into its individual, private exile, G-d still accompanies him. The G-dly spark present in every Jewish soul is also dragged down with the sin.
(Tanya)
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To execute the vengeance of G-d on Midian (Num. 31:3)
Rashi explains that one who takes a stance against the Jews is actually standing against G-d. Midian tried to fight the Jews by causing them to sin, enticing them with their beautiful daughters and their idols. The sins of illicit relations and idolatry were against the will of G-d; therefore, when war was waged against Midian, G-d was taking His revenge on them. We also see the great love G-d had for the Children of Israel, for even when they sinned and died in the subsequent plague, G-d took His revenge because Midian had wronged them.

(Likutei Sichot)
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Arm some men from among you for war (Num. 31:3)
G-d instructed Moses to avenge the Jews against Midian. Why, then, did Moses send other to fight the battle? Moses had lived in the land of Midian and felt it was not right for him to personally harm those who had treated him well. This is in keeping with the saying, "don't throw stones into the well from which you drank."

(Bamidbar Rabba)