Actually, if you look two verses later, it mentions separately ואת המלים אותם (those who circumcised them), and states that they were beheaded (whereas the mothers had their babies hanged from their necks).
Presumably, then, הנשים אשר מלו את בניהן means those who arranged for the circumcisions of their sons; they'd be the ones caught red-handed, so to speak, seeing as how usually they'd be the ones carrying the babies around. ואת המלים אותם, then, would be the fathers or the mohalim.
(Which isn't to say that some of these women didn't perform the bris themselves - as pointed out in comments, it is halachically acceptable, and we have other examples in Jewish history where they did so under extreme circumstances of mesiras nefesh, for example the story witnessed by the Bluzhever Rebbe zt"l recorded here - but I don't think this passage indicates that it was necessarily that common.)