So I'm playing the second time and doing everything i didn't in my first file..i wanna join the rebels this time and i know that in the end I'm going to have to attach solitude. i have my home and fam there if i did join the rebels will it affect house and fam

No, it wont.

No it will not, this applies to all homes you may own in other cities.

Logic would dictate that you move your family out of there before attacking that particular city.