If the Byz Empire has primo succession, than her first son (presumably also your heir) will indeed be her heir. But, if you get a new son after this, it'll be Born in the Purple, and become the new primary Heir for the Byz empire (special mechanic). It'll still be a member of your Dynasty on the Throne, and your heir will have a claim to the Byz Throne on succession, which you could press against your brother to unify the realms.
Since she's not of your dynasty (presumably), and gets a higher title than yours, she will not become your vassal (if you press someone's claim, they become your vassal if 1) title is lower than yours, and 2) they are either already your vassal, or of your dynasty).
She will have a Non Aggression pact with you, which you can turn into an alliance.