What will happen to my female guppy?

Your other female is most likely pregnant there's no way to tell until she starts getting big though. Inbreeding over a short period of time isn't bad but after a few generations it's good to mix in some different genes. What the other poster said about pecking orders is correct, if the one female starts to get aggressive again you could try to add a third female to even the odd and spread out the aggression a bit. Good luck with your fry!