I have often said that it is very important to remember that Mary and the disciples never really understood what Jesus was doing - at least not until he rose from the dead. Even they did not understand what He was really doing, or why he allowed Himself to be taken and executed. While they sure believed in Him and believed Him - they really did not understand the plan. Until. Until he rose from the dead. It was not just Thomas who woke up - they all did.
They had to.
As to Mary...
I can just imagine what went thru Mary's head and heart over those three days. She HAD to be confused and over-wrought with fear and, well, terror as the state put Him to death. I'm sure all she could do was 'cope', as I doubt she could understand.
Then, three days later, the whole universe changed for her and the disciples.