My witch hunter army is also a union between the Arbites and the sisters; the reason I have them working together is the amount of penitent troops in the WH army list. Arcoflagellants, and penitent engines are essentially convicted criminals who have been given a chance to redeem themselves in the eyes of the Emperor. My Arcos and PE's were all arrested and incarcerated by the arbites.
Sisters repentia, to a lesser extent, are also penitent troops. They aren't necessarily criminals, but they have strayed from the path of the sororitas. My back story for my repentia is that they were sisters who helped take down a cult that the Arbites couldn't handle alone.
In the process of dealing with the cult, however, the sisters witnessed the summoning of a handful of daemonettes. After reporting the incident to their superiors in the Ordo Hereticus, they were examined by an Inquisitor. While he could find no outward evidence that they had been tainted, he determined that their knowledge could corrupt their holy sisters unless precautions were taken. He ordered them to take the role of the repentia and further, removed them from the commandery and placed them in the care of the Arbites.
So my Arbites oversee the arcoflagellants, penitent engines and even sisters repentia. Of course, the Arbites do work with several confessors and priests who minister to both the Arbites themselves and to the inmates incarcerated within the precinct fortress.
I came up with the background because I wanted all of my sisters units to be faithful, and I didn't think it was appropriate for these avatars of purity to fraternize with the penitent legions. The Arbites provided me with a mechanism to keep the bad girls (and boys) away from the good girls.
I know this has already been a huge post (sorry), but if you're interested here's a link to more of the background material on my army- particularly the division between Precinct Fortress 17 and the Commandery of St. Katherine's Aegis:
The Witch Hunters of Escutcheon III
Also, omegoku, you mention that the sisters are out to get the xenos- it's certainly true that they often protect humanity from invading alien forces, but as the chamber militant of the Ordo Hereticus, they're more concerned with heretics, mutants and witches than they are with aliens.
When the Inquisition attacks alien species, it's usually under the jurisdiction of the Ordo Xenos and their own chamber militant, the Deathwatch Space Marines. Unfortunately, gw chose not to give this Order of the Inquisition it's own codex.
However, if a human- say a government official or an officer in the Imperial Guard, or a representative of the Ecclesiarchy was found with alien technology, that might indicate membership in a cult... Heresy. Enter the Witch Hunters, and with them, the Sisters.
The Eldar race has been known to deal with certain humans for their own obscure purposes, and everyone knows that the Eldar race is ruled by witches. Any human who dealt with this enigmatic race would certainly be suspected of witch craft.