So just the machine, without the "pilot"? Personally, I'd actually recommend going to the AdMech for this rather than the Ecclesiarchy. Chances are it's much easier to get one from them. Unless, of course, the Rogue Trader in question has good contacts to a corrupt Cardinal who is willing to break protocol.
Personally, I see Penitent Engines are somewhat on the same level as Arco-flagellants, and even for Inquisitors it may be difficult to acquire them:
"Arco-flagellants are normally used by the Ecclesiarchy's fighting forces in suicide attack units. However, an Inquisitor can request (or demand, if they are confident enough) that a Cardinal turn over an Arco-flagellant or two to their authority. As the Ministorum holds those Inquisitors who possess a more radical turn of mind in some suspicion, it is usually the more puritan and outwardly pious agents of the Inquisition who will be able to include them as part of their warrior band."
Of course, as fluff is chiefly a matter of individual interpretation and personal preference, there are no hard rules for anyone's own game - but I think looking for alternate (and, as some would say, even heretical) ways to acquire such a piece of technology would keep more with the spirit of the setting than just walking up to some normal cleric and asking for a favour. This could take the form of backroom deals with the Mechanicus (who doesn't really like the Ministorum anyways, and may actually have different versions of the Penitent Engine they use for their Skitarii) or even shady deals with a corrupt Ecclesiarchy priest who wants to get rid of a political rival, a popular sect which threatens his/her powerbase, or even wishes to acquire something exotic that only a Rogue Trader could smuggle into Imperial space…
As far as profit factor tests are concerned … yeah, I guess that would be one way to do it - but I think the crew might miss out on some interesting RP if all of this is reduced to a dice roll. Political intrigue is a major theme of Rogue Trader gameplay, no? And think about the possible consequences - it's almost an adventure in its own right!