When it rains, it pours...funny how that happens, isn't it?
Based on what you have written, I have to agree with TheHardFlaccid. You both agreed to a FWB arrangement with no indication of exclusivity therefore you are free to see others; just as she is.
It is admirable that you have concerns for your FWB feelings but her low self-esteem issues are not your responsibility to repair. And if you remain with her simply out of guilt or obligation (for losing your virginity with her), you will likely grow to resent her and that is not fair to either of you. If FWB wanted a serious relationship with you, she needed to tell you that upfront and allow you to make that choice. She didn't; therefore you are not the only one accountable here.
Besides, you may spend time with the second girl and discover you two really don't "click" after all but you won't know that until you spend a bit of time with her.
If it is really bothering you, then perhaps you can let your FWB knows what's going on although with a FWB relationship you are not really obligated.
Whatever happens; be sure to use protection. Always.