So in the acolyte cell in the new campaign I'm running, we have a renegade psyker who dropped out of the schola progenium when he began to manifest his abilities, a jeretek assassin from a forge world who is at least willing to use if not obsessed with Xenos technology (especially Necrons) and a noble born assassin. I'm thinking the Inquistor must be a radical of some sort, potentially even a Phaenonite? I was considering having a Phaenonite inquisitor as the campaigns villain, perhaps the players should be his acolytes instead?

What's special about the highborn?

I think the only potential issue would be the heretek, but as you say this can be easily resolved if you simply give them a Radical master.

The psyker's background actually makes total sense. The Schola Progenium does not condone psychics among its students -- or rather, they immediately transfer them to the Astra Telepathica once genetic testing reveals their true nature. Any Inquisitor could have picked him up, either on the Black Ship or by personally travelling to the Schola where the character was held in captivity awaiting deportation.

Of course, the Inquisitor still needs a reason to recruit this psyker, but this can easily be generated by pointing to his psychic evaluation, his family background (given that only the orphans of Imperial nobility and ranking adepts become progena), and/or his potentially promising track record and psychological profile of his first days/weeks at the Schola.

I don't know a huge amount about the Noble Born's backstory yet, but here's what I was intending for the first mission (keeping in mind that this was written from the idea of having a puritanical or at least moderate inquisitor:

The mining world of Scarth has recently experienced a high upsurge in psykers in the last few centuries, directly related to the mining of a local mineral known as corcase athex. Athex is highly sought after by the Mechanicus for its application in constructing superior warp drives, but the side effects of mining it result in a high rate of mutation producing the psyker gene in those that come into close contact with it. Additionally, the mineral can be used to manufacture a variant of spook, referred to as "case", which is a highly valued if illegal local commodity.

The original plan was for the acolytes to be assigned to the world of Scarth to bust a case ring before the arrival of the Black Ships to take away the world's tithe of psykers - for the second time that century, an unheard of event. While on planet, they would not only discover that a local miner's guild had formed a collective with the aim of escaping the Black Ships, but also that the acolytes of a Monodominant inquisitor were on-site an attempting to sabotage the mission, with the aim of befouling the reputation of the acolytes' inquisitor, who is a psyker. The Monodominant Inquisitor would later on in the campaign be revealed as a Phaenonite, who was trying to discredit the acolyte's inquisitor because their Inquisitor was investigating him.

However, now that we know that a radical inquisitor would be the best fit for this acolyte cell, would it be better to have them as the sabotage cell working for the Monodominant/Phenonite as opposed to the previous plan? That way the other acolyte cell can serve as a foil/antagonists. To keep his identity a secret, the inquisitor could report to them through an interrogator or senior acolyte.

Curently trying to get a game started with an Ecclesiarchy priest with (unlicened) psychic powers, wich he explains are miracles and manifestations of the Emperor's devine will. Also he looks like the 40k equivalent of a creepy old man wearing mirror shades and an amish stetson hat.

Any inquisitor who would take this chap for an acolyte would have to be a radical at least.

What kind of senior acolyte do you think a Phaenonite would use as a go-between between him and his acolyte cell? I was thinking perhaps an assassin, arbitrator, psyker or adept, with some radical elite advances like "Mark of the Phaenonite" and maybe "Warp Dabbler".

Or something completely innocuous - why pick something everyone would expect? That makes things more mysterious for your players, too, because they won't know who they are working for or exactly what philosophy they are helping.

Perhaps they are told by their Interrogator that there is a rival cell of radical Acolytes that are attempting to cover the whole ring up... When in reality, they are the servants of a hard line Inquisitor who are there to investigate the involvement of the PCs Inquisitor.

You know, I ask that very question every time I sit down to play and look at my group

To be fair, the Xenos unsanctioned psyker has been picked up at the start of this mission as a mercenary to help them blend in on a deep cover mission. After all, anyone accusing a group visibly consorting with alien witches of being part of the Inquisition is clearly insane!

It should be interesting when they find out that the Inquisitor who said that they should complete their mission "by any means necessary" has been killed and his replacement is a fresh-faced burn-the-heretics type puritan. Shenanigans will undoubtedly ensue.