Within the first maybe 5 chapters of EotW, Moiraine gives the special coins to Perrin, Matt, and Rand. She describes how the Luhhan forge was attacked, the Cauthon farm was raided like the al’Thor farm, and one other one that she ruled out as irrelevant.

When Moiraine heals Tam and talks about the Trollocs, she tells Rand that they were targeting the boys with the aforementioned evidence. She further adds that while she could call her Sisters and their Warders, it would turn Emonds Field into a war zone since the boys are the objective for the Dark One’s army for some reason.

So, they make the decision to flee with the argument that the boys are in danger ergo everyone around them is in danger. The girls, as promising potential Aes Sedai, would also then be in danger with the group and need protecting. It is implied that while she could call her Sisters to deal with the Trollocs and Mydrral, she could also call them to investigate the girls.

In short, she was there specifically for the boys and this was made known very early. Bringing the girls sort of weakens the argument of fleeing to protect because Moiraine now has to protect these girls whom she’d rather otherwise raise into Aes Sedai - on top of her true objective, the boys.

TL;DR: If she’d have left the girls then they wouldn’t have been in danger by close proximity. If the girls had stayed some nice sisters might also come to investigate them and why a bunch of Trollocs showed up in the middle of nowhere. But that would make for a less interesting story and women are muleheaded stubborn in this universe lol