To simplify everything since this no matter how many sites it has, it is still a single company approximately with 20 users. I would create new user accounts for those in site A onto the DCs in Site B. Then have a 2003 Server in Site A (dcpromo-ed) to the same domain as Site B.
This will simplify management as a whole instead of dealing with it as single site entities.
Each system at Site A, I would have the computers added to new domain.
Each user at Site A would log into the new domain (to create profile entry) and then log out.
Modify registry on system to point their new SID to their old SID profile location. (if needed)
Modify ntfs permissions for new SID to old SID folder within documents and settings. (if needed)