If Emma knew who Marian was, there would be two respectable options:
1. She would have saved her, anyway. Had she known the entire story, and it involved the knowledge that Marian would die that night, Marian’s influence on the future would have ended there. So, saving her by bringing her to the present, would most likely not directly affect how time unfolded in any large or discernible way (with the loose concept of time travel that OUAT is using). Considering, she’d already change large elements of the past, it would be difficult to leave this woman to die if there was a strong possibility that she didn’t have to. So, yeah. Emma would save her, because the relationship that her frenemy has gained through killing (which would probably the case) Marian, an innocent woman is not as important as saving Marian. I would personally have a lot less respect for Emma if she decided that Regina’s relationship did mean more.
2. She would have left Marian, but told Robin what Regina did. And OutlawQueen would be over. You think you’re angry with Emma now? Had that happened, I know that many would flip their lids. And it would be worse, because Regina would have no defense for her actions, no means to continue their relationship, and no alive Marian to make her seem like a better person, or make Robin feel better about even being friends with Regina.