Your theory is reasonable. Luffys mother being a bounty hunter sounds good. But she doesn't necessarily a D. Roger marrying another D doesn't mean Dragon did. The one piece wiki says luffy was born in fuusha village. So it's highly probable she was a normal person. Or an idealistic runaway aristocrat/noble like Sabo. Or maybe a tenryuubito who got lost in the Goa kingdom on a visit and dragon helped her.
Regardless of whatever you're theory about her is, you should know there's always the possibility she was killed or died in some way and this may somehow triggered Dragon's rebellion.
Regardless of whatever you're theory about her is, you should know there's always the possibility she was killed or died in some way and this may somehow triggered Dragon's rebellion.