It wasn't that Peter was a Wiggin alone that induced his rejection, it was that the I.F. was running out of time. The attack forces would be arriving at their targets soon and they desperately needed to find and train a commander for the battles to come. Peter would have been accepted in other circumstances if Mazer Rackham is to be believed. In Shadow Puppets Rackham says to Peter:
"No, Graff looked at your tests and watched what the monitor showed us, and then he talked to me and showed me, and we realized: You weren’t what we wanted as commander of the army, because people don’t love you. Sorry, but it’s true. You’re not warm. You don’t inspire devotion. You would have been a good commander under someone like Ender. But you could never have held the whole thing together the way he did."
Given how Peter treated Ender during his childhood it was plain that they both couldn't be in Battle School together. So they commissioned a third child from the Wiggins and lucked into Ender.
Valentine was said to have similar abilities to Ender, but tested as too pacific. From Ender's Game:
"I interviewed Colonel Graff when he arrived from the Battle School. It is his best judgment that nothing these children [Peter and Valentine] have done is out of their reach. Their abilities are virtually identical with the Wiggin. Only their temperaments are different. [...] Graff says the girl was rejected for Battle School because she was too pacific, too conciliatory, and above all, too empathic."
So it seems unlikely that Valentine would have been sent to Battle School under any circumstances. She certainly could not be there at the same time as Ender since she acted as Ender's protector and Graff wanted Ender isolated.