If a Jewish Man has intimate relations with his wife, and then the seed escapes the woman's body she becomes known as a Paletes Shichvas Zerah. Now, if that occurs within 3 days she becomes Tamei. If the seed escaped after 3 days then she's Tahor and it's fine. However, if she has intimate relations with a Goy, then she never becomes Tamei no matter when the seed escapes from her body. Being that the reason why men would separate from their wives 3 days before Matan Torah, it makes zero sense to say they had to, because, they weren't Jewish anyways! So what's the pshat?
One could easily argue that they were fully Jewish not on the 7th of Sivan, but on the 4th. After all, we learn the halachos of conversion from Har Sinai (Yevamos 46b), and, according to R’ Yosi, they washed their clothes, toveled, and sprinkled on the 4th of Sivan, and so they had to have three days (Shabbos 86b-87a).
The Gemara ibid. 86a makes this point explicitly: the one who holds that she’s impure for three days holds like R’ Yosi, and the one who holds that she’s impure for just two days holds like the Chachamim that they separated on the 5th.