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I am running an campaign in Dark Heresy with a group of Initiates of the Ecclesiarchy, instead of Inquisitorial Acolytes. The team is a Sister Hospitaller, a Red Dead Redemptionist (ayuck), and a Witchhunter type of Cleric. In my previous campaigns run with Acolytes, I have had players that enjoy roleplaying Skill or Talent developments, like cleaning their gun more thoroughly after taking Basic Weapon Training or spending downtime during travels reading a relevant Imperial text before taking a Common Lore, oh or preaching to a ship's crew frequently before taking Air of Authority (true story bro). For Acolytes that like to roleplay having books or files before taking a Lore Skill, it was always easy (relative to being Inquisitorial Agents) to justify a player having a forbidden tome when roleplaying to take a Forbidden Lore. The problem I have run into recently in that I have the Cleric wants to like texts that his character could study to learn more to fight the forces of evil, be they heresy, chaos or xenos. The characters started the campaign with the usual "no prior knowledge of Chaos," so the Cleric mainly wants to learn more about heresy and what is heresy, etc.

Both my player and I are well versed in 40k lore but neither of us can figure out where members of the Ecclesiarchy get such information from? Unlike an Inquisitor, we don't see how a Bishop or other clergyman would have access to such forbidden works or if they are non-forbidden types of books within the church or Imperium that hold such information. Do you imagine certain agents of the Ecclesiarchy having hidden archives of forbidden knowledge; kept for the sake of protecting and guarding from those who would abuse the knowledge? That is like the only idea I could come up with. Do any other Dark Heresy GMs have any suggestions?

For Holy Terra:

"The Ecclesiarchy has guided the servants of the Emperor for nearly ten thousand years, but deep within its ancient records its beginnings can still be traced. In the miles of catacombs beneath the Ecclesiarchal palace, the dusty journals of past Ecclesiarchs nestle next to scrolls containing the confessions of heretics and blasphemers. Deeper into the library, fully a day's walk from the nearest secret entrance, are the chronicles of Lord Vandire. Even further still is the Vault of Origins, where the earliest records are kept.
Dating back to the Horus Heresy, most of these scripts are kept within pulsating stasis chambers, their pages so brittle that they can never again be read or turned. Their beautifully illuminated and illustrated leaves are cracked and torn with age and the letters have faded into indistinct greys.
The secrets of the Vault of Origins are imparted only to the most high-ranking officials of the Ecclesiarchy. Even the Inquisition are denied access to this burial chamber of history, lest they destroy the Ministorum's glorious past in their quest for knowledge and truth."
- 2E C:SoB

Ophelia VII is also said to have vast dungeons and archives containing the confessions of many millions of sinners, though I assume any larger Ecclesiarchal site (such as a sector cathedral) may have a library of sorts.

Your players may also wish to schedule a trip to a convent of the Orders Pronatus - a Minoris branch of the Adepta Sororitas partially concerned with trying to unlock the secrets of xenos technology and Chaos artefacts in an effort to better understand how to fight the enemy as well as simply keeping them locked away:

"The Orders Pronatus specialise in retrieving, guarding, studying and repairing artefacts of value to the Ecclesiarchy. This includes the uncounted thousands of holy relics revered by the people of the Imperium, but also relates to items captured by Imperial forces which are too powerful or significant to be allowed to fall into enemy hands. They also have the responsibility of maintaining and blessing the many banners and symbols of Orders Militant, as well as being called upon to reconsecrate the livery of other Imperial bodies (such as the Chapter banner of the Lamenters Chapter of the Adeptus Astartes after its involvement in the Badab Uprising, the banner now called the Banner of Tears). Some Orders Pronatus are known to have given all in the defence of the artefacts they guard or study, and the fate of the Order of Blessed Enquiry is a salutory lesson in the risks involved with the evil of the Ruinous Powers, even if the intent is to safeguard Humanity from their corrupting influence."
- Liber Sororitas, WD #293 <sidenote: the Order of Blessed Inquiry was the convent of Parnis featured in the graphic novel Daemonifuge, it became corrupted by the Keeper of Secrets they kept for study>

And last but not least the Ecclesiarchy's Technology Purification Centre, also located on Ophelia VII:

"Thor's treaties, made before the creation of the Convent Sanctorum on Ophelia VII, allowed Mechanicus supervision of all Ministorum forges and equipment maintenance facilities in the Convent Prioris in return for permanent loan of the machinery necessary to produce the power armour and bolters that Ecclesiarch Vandire had ordered built for his bodyguard. The Mechanicus agreed hastily, foreseeing a virtual stranglehold on the Ministorum's mechanical resources and intelligence.
They were mightily displeased when Thor later opened the Convent Sanctorum and transferred much of the Ecclesiarchy's technology facilities there, including the valuable Missionarus Galaxia technology purification centre, which oversees the investigation of equipment discovered by Explorator missions. Never on the best of terms, relations between the Mechanicus and the Ministorum were soured considerably by this development. Yet, the Mechanicus found it impossible to retract their commitments to provide weapons and armour, and on Thor's orders the Ecclesiarchy has since been relatively trustworthy in providing to the Mechanicus details of newly recovered technology."

That should give you a few ideas, maybe.