Regina is just striking out at her step grand daughter/co-parent because Emma appears to have her "happily ever after" and Regina doesn't ... yet.
What she needs is a heart to heart with Snow White, her step daughter, on having faith that if Regina & her soulmate are meant to be together, they will end up that way.
What better obstacle to place in her path than a returned wife.
Who knows, maybe she and Robin had a "row" and Marian left their home in the forest to live back home with mom & dad. Robin felt guilty about the "row" and that she went missing while living with his ex-inlaws.
Recall, Marian kept her mouth shut so Regina didn't know who was being executed in her prison. That suggests mom & dad never found out why their daughter didn't come home one day. For all her parents knew a wolf could have taken her life or she could have run off with a dread pirate.
As for consequences, if Regina even understood Swann's motivations for bringing Marian back... i.e not to screw up the timeline again, she might have been more specific with Emma.
"Miss Swann, you assumed that Marian would die in my prison the next day. But what if she didn't? What if her parents arrived and ransomed her? Or if she admitted who she was and told me where Snow was and I spared her little pathetic life? What if her death in the prison affected another prisoner and he changed his mind and confessed his part in Snow's disappearence, thereby allowing me to commute HIS sentence?
Then by removing Marian from my dungeon you HAVE altered the time line, the one thing you claimed you were trying to avoid in the first place. Lets hope my broken heart is the only casuality of this action."