The majority of those that left a response said they would choose "option one." If you selected "option one" and well managed your relationship development and engagement processes, then helping "Mary"--the stakeholder in question--and her team contribute to the change should be beneficial. Why?
The first thing to consider is that Mary would be a key stakeholder at several different levels in the overall change management program.
As a long-term employee leading a group of workers, she is a stakeholder in the overall organization and is likely to have many unofficial contacts and significant influence.
As the leader of a group of workers who will be disadvantaged by a planned reorganization, she and her team are critically important stakeholders for the change manager. The group will never like the consequences of the change, but they need to be included so they at least cooperate for the good of the overall organization.
Because they can contribute knowledge and support, Mary and her team are also stakeholders of the program and particularly your project. The assumption that your team has enough knowledge to bypass her people is risky. You don't know everything that happens in Mary's section on a day-to-day basis.
The second important consideration is where the value is created. Ultimately, there is no value to the organization unless the change is successfully implemented.
Your project may deliver a key component needed for the reorganization but if it is not used, there is no value. This is something IT people in particular need to remember; 99 percent of IT projects require changes to business processes and are a complete waste of time if the business people reject the new processes.
If you selected "option two" and chose to ignore Mary, she is likely to become an active opponent of the change (no involvement equals no commitment and no support). This puts your most important stakeholder at a disadvantage: the overall change manager.