In my opinion, there are at least two reasons that Christine de Pizan choose to make the Amazons side with the Trojans rather than the Greeks.
On one hand, the Greece was more powerful than the Troy at that time. Arranging Amazons in the weaker side could highlight their bravery, belligerence and adventurous spirit. Instead of Troy, they tended to challenge the powerful Greece.
On the other hand, it showed the chastity of Amazon Warriors. Penthesilea kept virginity because she thought most of men couldn’t match her. But when Penthesilea heard that Prince Hector who had the same qualities as her, she began to love him. After Hector was killed by Achilles during the war, Penthesilea looked at Hector’s body in a temple and Swore to avenge him. And then she fought until dying. By depiction of this, Pizan displayed the precious virtue that women should be loyal and faithful to their lovers.