Cobel is not our friend.

She isn't about to just switch sides all of the sudden. She doesn't care about Mark, she has her own motives.

Cobel spent the first few episodes of S1 trying to find Petey. She spent much of S1 trying to prove reintegration is possible, and that severence is not 100% infallible.

She needs to prove this to the board so they will realize they DO need her, as the technology's inventor.

Now she has proof, and will befriend Mark as long as she needs to bring him to Lumon. Mark will be her bargaining chip.