3 reasons why Sisters should stay as the Chamber Militant of Ordo Hereticus:

1. Ordo Hereticus is different from Ordo Malleus and Ordo Xenos, they are closer to the real Inquisition than either of the former ones. Ordo Hereticus working with the official army of Adeptus Ministorum works great thematically.

2. It gives a better reason for why the Sisterhood is allowed to exist. Originally the only reason was the infamous loophole "no men under arms". Currently the reason is that Ordo Hereticus, which was formed at the same time as Adepta Sororitas, made a deal with Adeptus Ministorum, letting Ministorum have Sisters of Battle as their official army if in exhange the Sisters become the Chamber Militant of Ordo Hereticus, keeping an eye out for corruption within Adeptus Ministorum.

3. It gives all three major Ordos a Chamber Militant. Deathwatch was invented in 3rd edition too.