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I'm not sure if this is the best place for this stuff, but let's go:

The Ardentus Argentum (so called because they feel strongly about stuff and are silver) are my new homebrew chapter/legion. Their story is somewhat similar to the Celestial Lions - they saw the Inquisition do gak and were all like 'nope, that's bad, we ain't doing dat shiz' and proceeded to get uber-rekt by the Inquistor's battleships. The only way to escape complete destruction of the chapter was to flee into the warp. It didn't go so well and even more of them got nommed/rip'n'torn/raped/mutated/AIDSed and so not that many are left. Those that are left are in fact loyal to the emperor. Sort of. They don't revere him as the godly figure that the Ecclesiarchy hype him up to be, but do share in his original vision of peace across the galaxy, while not being quite so anti-xenos and anti-mutant. They also believe that rather than exterminating heretics, rehab programs might be better solutions. BUT. And it's a big one, in order to successfully survive the terrors of the warp, they did sort of have to turn themselves to Chaos a little bit. And while they don't want the galaxy to burn or to be made a servant of one of the Dark Gods, the marines do realise that doing so is the only way they can survive and potentially grow to work against Chaos in the future, and that they need all the help they can get in combat after being slaughtered and gribblied by Inquistion and Daemons alike. They show up every now and then to aid Imperial forces againsttheir foes (and quickly run away before they get attacked), but also assist the Tau, Eldar, AdMech and sometimes Orks against Chaos forces, Necrons, Tyranids and even other Astartes, and so are branded as a traitor legion by most. They recruit mostly from worlds they defend, who see their non-radical, everone-be-nice approach to be way better than Imperial rule/mass slaughter by Chaos forces, but also take on stragglers and outcasts of both loyalist and traitor legions, provided they aren't too extreme.
Overall these guys are sort of like Malal Marines + Reasonable Marines? I guess? Other stuff includes the fact that because they were quite open and reasonable and not so purge-mad as most other chapters, they are a damn sight friendlier towards alien races, and the chapter master is such a shrewd diplomat/ they sometimes just act as mercenaries to Tau, Eldar and Admech, they treat all ally rankings on the chart as being one better (except 'Nids), and because they've all been taught to get along, not all models in a unit must bear the same mark. Two things I'm not sure on though are thus:
1. Champions with Marks/ marked units in general: These guys aren't Chaos worshipers that want a new dawn of Heresy in the galaxy. They don't want everything to burn. However I do want some of them to be dedicated somewhat to the Dark Gods. I've got an idea for one sergeant who got so angry over badly treated some people were and how some space marines just didn't care about casualties, even civilians, and at one point ended up defending such innocents so wrathfully that Khorne saw him and went 'damn, I like this guy' and gave him a mark that now turns this guy into a bloodthirsty animal in combat, even if he himself doesn't want the 'gift'. Also, maybe Tzeentch said 'bet I can show some cool magic stuff' and some guys just went along with it but how do I justify people having marks of Nurgle and Slaanesh? And how do I generally explain the fact that these guys had to turn to semi-Chaos in the first place?

2. Cultists: These guys make a lot of use of 'cultists', as they go 'hey! These guys who saved us offer an actually pretty decent standard of living and aren't evil pricks like 90% of everyone else! Let's go side up with them!' Now these guys aren't strictly cultists in the normal sense, but that's what they approximate in the codex. As I write this the more I think it should go in the modelling forums but while we're here let's do it - the current GW cultist models are a bit too mad and evil for me, and I don't think the majority of their recruits are going to be guardsmen, so I'm either looking for a convincing lore-friendly reason why the counts-as-cultists would have to wear the stuff the cultist models do now, which is just unnecessary for essentially average hive dwellers, or suggest any not-that-chaosy, not-imperial-guardsmen models that could be used for my not-cultists-but-whatever cultists?

First of all I would suggest this be moved to 40k background if you want fluff and lore help.

Anyway, in general I would suggest you model your home brew after the Alpha legion; they were a loyalist legion that turned chaos to attempt to stop chaos, I would definitely recommend reading into their fluff.

Now to your questions:
1. If you want to give them marks it might be better to go along the path that, although tgey started loyalist, their time in the warp has tainted them and turned them chaos; this would also be more fluff friendly as no mortal can resist the touch of chaos whilst in the warp. You could have your Warlord/Chaptermaster staying loyal if you think he has the strength.

Here's a little secret: no one can turn half-chaos, once chaos has you you are gone.

2. An idea maybe to mix guardsman and cultist models together in squads to show that there are a mix of renegades and extremists. But if you really want more every day recruits you might have to look for 3rd party models :O.

But once again I would read into the Alpha Legion, they show that the warp will taint you no matter your intentions.