Yes to all that. 
She did have a choice once but that was long before all that happened. 

The last thing we see is John's shocked face after Sherlock collapses in the flat. We never see her offering or understanding anything. This is pure speculation. What we see, however, is her starting to bicker the very moment she thinks John has forgiven her. 

Well, she could. She could keep nagigng him if she wanted to. From the dialogue it seems she didn't. 

But we've discussed this before recently. I think the conclusion, as I see it, is that our interpretation of her behaviour is filtered through our view on the character to begin with. 

If we keep it strictly to the facts, we know very little about what happened in the months between Sherlock’s collapse and Christmas. We know Sherlock spend part of that time in hospital and we know the Watsons have not been talking much form Mummy’s and Mary’s comments, respectively. Everything else concerning that time is indeed pure speculation. The only thing we can do if we want to discuss about it is to make educated guesses based on our understanding of all the involved characters. Depending of our preliminary understanding of the character(s) we will end up with different scenario’s which we deem “most likely”. I think it is very hard to interpret something we have not been shown, without getting a bit more in detail about the characters motivation.
Personally, I think it was indeed John who “took his time” to figure things out. We know since TEH that John has to work through issues before he can forgive. For Mary, the time waiting for a “verdict” must have been hell. I already laid out my guess of what might have been going on in her head and I would not be surprised if the lash-out we see at Christmas was not the first one. But both her and Sherlock seem to have handed the reins to John in the matter of forgiving her. To get back to gently69’s point, I think as far as Mary was concerned, she had lost John the moment Sherlock revealed his “trick” to her in Leinster Garden’s. She seems convinced that as soon as John would know the whole truth of what is hidden in that USB stick (I will just assume there was evidence on there for now), he would stop loving her for good. She cannot hope for his love, but she can still hope that he and Sherlock will help her (and the child), so she stick around and waits.
Her behaviour after the reconciliation to me seems very much in line of what we see between her and John in TEH, this bantering seems to be how they interact. So her going straight back to it seems to me to be an attempt to restore somewhat of a normality between them.
 

Lola Red wrote:

Her behaviour after the reconciliation to me seems very much in line of what we see between her and John in TEH, this bantering seems to be how they interact. So her going straight back to it seems to me to be an attempt to restore somewhat of a normality between them.
 

I wish I were better at posting screenshots ... Because if you look at John's face during the bickering in TEH and during the "forgiveness" scene in HLV, there is a huge difference in how he looks. And I doubt that Martin I-can-do-that-line-with-a-look Freeman did that accidentially or just forgot to look happy.

tonnaree wrote:

Schmiezi wrote:

Lola Red wrote:

Her behaviour after the reconciliation to me seems very much in line of what we see between her and John in TEH, this bantering seems to be how they interact. So her going straight back to it seems to me to be an attempt to restore somewhat of a normality between them.
 

I wish I were better at posting screenshots ... Because if you look at John's face during the bickering in TEH and during the "forgiveness" scene in HLV, there is a huge difference in how he looks. And I doubt that Martin I-can-do-that-line-with-a-look Freeman did that accidentially or just forgot to look happy.

Agreed.   You can see so much in Martin's face and knowing how expert he is I can't believe what we see is not intentional.
 

Slight misunderstanding. I did not mean that there was an immediate return to normality, merely an attempt of one of the two parties to get some aspects of that past normality back. I doubt that their relationship will ever be again as it once was. John might be able to forgive, but I would be very much surprised if he would ever forget.
 

Liberty wrote:

Maybe I'm overthinking - it might be just that it was written to tie into the Christmas setting of the finale. 

I don't have an answer to your question, just one thought:

The writers have planned the entire series before writing it. If they wanted the "forgiveness" scene to take place at Christmas, but with John making the decision sooner, they could have altered the timeline in several places.

So no, you suely are not overthinking here.
 

mrshouse wrote:

Maybe the Christmas setting was just supposed to add to the joy of reconciliation.

Do I detect a hint of irony? 

I think it's fair that the fireplace scene wasn't necessarily a very happy moment for John. I know a lot of people think that is the scene where John forgave her. That is not how I view it. I view that scene as John telling Mary that he has chosen to start the process of forgiving her and re-building their relationship and life together.

Thus, it's more a moment of choice and determination, not the moment when all is forgiven and forgotten. 

To me, it's the most obvious when he says that he is "basically stilled pissed off" with her and that "it will come out every now and then". That tells me that he hasn't forgiven and he most certainly hasn't forgotten. But he won't pry in her past, and as long as she is open and honest with him in the future, he is willing to go down the road of forgivness with her.

That is how I interpret that scene.