The general thing to keep in mind when designing your own army is that you can do ANYTHING. The Sons of Horus had about 30,000 people in it. Loyalist marine armies are usually based around companies which contain 100 people. It's perfectly acceptable to have 100 or so marines didn't feel like following Abaddon.
One question, did they join Horus in the heresy then refuse to join Abaddon. Or did they go against Horus and not participate in the heresy at all?
If they did participate in the heresy:
this presents no problem as once Horus died it is absolutely acceptable that a few of his captains went their own way. Abaddon didn't hold that much sway after all. It would be very hard/impossible to say they are still part of the Imperium. Maybe a neutral company or part of chaos but not Imperium. They could still be loyal to the emperor I guess...
If they did
not participate in the Horus heresy:
this means you will have to write some pretty convincing fluff as to why they betrayed their primarch. Maybe they were horrified by Istvaan and fled to the emperor asking for redemption. If they had personally been redeemed by the emperor (not yet dead/dying) then the Inquisition would not dare touch them after the heresy. They could still fight as a chapter, would also justify use of the "we stand alone" trait as no-one else trusts Sons of Horus.
Alternatively you could just field them and claim they are based around pre-heresy time period. No-one would object tto your fluff in a game.
Just remember when it comes to fluff anything goes. Try not to contradict any GW fluff but fell free to do whatever you want, no-ones going to complain, except the Ultramarine players, they fight viciously in fluff attacks on their chapter. (funny incident on the GW forum a while back
).