Cat problem, socialising a stray?

I found a stray 6 weeks ago. A neighbour called thinking she was my cat Ruby who went missing 4 months ago. It wasn't her but I took her in as she was covered in parasites and her long fur was falling out, she was thin as a rake and in agony. I have been doing my law finals revision for the last 2 months, so I have spent about 2 hours a day with Grace (the name I gave her) I think she benefitted from the peace quiet and routine and she has blossomed, been treated for the critters and is in my outhouse which is warm cozy, furniture just like another room in the house really. I didn't want an infestation in my home and more imprtantly my boy cat fatty, son of Ruby is in the house. Fatty is the softest and sweetest natured cat ever, he helped his mum look after her second litter of kittens and is an absolute angel with other cats, he is such a happy little thing and I din't want him to feel dominated in his own home. Grace is also a softie, with me....but I have been bringing fatty into the outhouse every morning for half an hour. First time, he went up to her carefully but excited to find a new friend (he is spayed by the way so I know she cant be in fear of that) He's very careful to not appear threatening to her, very cautious, doesnt make eye contact and turns his back slowly to her which I know is a sign of trust, and a signal they want peace. Thing is she gets really funny with him, low growls and miowing loudly, although she hasnt tried to go for him, she's really not the type, you can tell shes been mistreated because she freaks out about really odd things like when I picked up a chair to move it once. Not sure whether these morning introductions are doing more harm than good, fatty is very quiet when he gets back in the house and just gives me this sad look. I really wanted to give her a home but I can't bring her in the house and I can't keep her in the outhouse forever she needs the kind of tender loving care I am giving her but from someone with no kids and no other pets...I think. What doesn everyone else think? Any experience of this? I want them BOTH to be happy, and I'm not prepared to compromise fattys happiness. I know If I got a kitten or something fatty would be all over it and theyd be best friends, I also know he's like to be friends with Grace,it's just not fair on him, or her. is there any hope here?