As a update, I sat down with both Player-A and Player-B and we discussed options and ramifications. While I was still willing to accommodate them if they felt that actively &/or strongly about it (as both a reasonable GM and their friend), it was ultimately and mutually decided that they would play Astartes characters.

Fair enough.

Just as an aside - I have GM-ed several games which mixed Astartes and non-astartes - both Deathwatch, Black Crusade, and Dark Heresy (Grey Knights). My tuppence ha'penny on the situation:

If you ever want to do so, don't worry, it works fine.

Ascension-level Palatines are quite capable of running with astartes, and - arguments about whether angelus calibre weapons should exist aside* - manage perfectly well. Influence (rather than reknown) lets them acquire some random toys which close the gap a lot (and arguably push them out the other side); the Mantle of Ophelia, for example, gives you the unnatural toughness you normally lack. A Godywn-Deaz may be less powerful than an Astartes-calibre Godwyn, but it's also reliable, which a Godwyn isn't. Being able to fire automatic bursts indefinitely with zero risk of jamming is important, and it's perfectly capable of murdering hordes without needing to roll dice for the damage done by a hit.

Equally, you can make a suprisingly lethal opponent even with lower stats if you learn to use the tactics available to you rather than just "we stand in a line and use semi-auto bursts". Yes, marines can 'catch up' and requisition better guns, but you can always be ahead of them on skills. Things like Wall Of Steel & Counter-Attack paired up with a Best-Craftsmanship balanced weapon are easy enough to get out of the bat - and with a Defensive Stance, you don't even really need to attack - just let your opponent come at you and stab them with free attacks as they overextend themselves.

Crushing Blow and Mighty Shot go a long way to boosting up damage (again, yes, marines get them eventually, but you get them from day 1 if you want them), whilst.....I can't remember the name - there's a ranged damage hatred talent available to the palatine (heroine of the order - just checked). Throw in the celestian elite advance where you hate everybody, and you've got a nice equivalent of deathwatch training, but a bit better (because it also gives you Proven [3]).

Not all the faith talents require you to have the sister working as 'mobile miracle dispenser', either. I understand why Lynata dislikes this effect, but you can avoid it. Holy Light, Holy Radiance, etc, can all get stuffed. If you want a true militant sister, Wrath Of The Righteous allows you to trade a fate point in for +1D5 damage (okay but not amazing - but you do get lots of 'spare' fate points thanks to the talents) but the real gem is the 'burn a fate point' option (Miracle Worker)- the thing that makes a palatine scary is the ability to spend a fate point to gain the 'burn' effect - in this case; cause the maximum possible damage for the weapon you're using, plus an extra 1D10 on top.

Our sister historically first used that with a Multimelta and unloaded over 50 damage into a Carnifex with a single shot.

If you have access to daemonhunter, there is an elite advance (Pyroclast) which allows the character to use a grey knight incinerator and ignore the 'astartes only' restriction - It's worth a look.

Narratively, we used the Sister as an especially militant inquisitor. But she worked perfectly well alongside astartes, and showed them up on more than one occasion.

The main problem for the group in game is having your best commander (because a militant Palatine will almost certainly have command and command talents out the wazoo) doesn't have access to squad mode and doesn't provide any cohesion.

* Personally I'm in the category of 'yes', but that's because even if you disregard FFG I consider Black Library published stuff just as valid as the GW design studio and the first print of the Inquisitor's handbook was a BL book.