Letters to the Editor
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Cary's right
It does seem you love her, make sure you know where your girlfriend stands. She might be using the move to Berkeley, where she may think you can't follow, as a gentle way of moving on. Especially since she informed you she would not move for you...
You need to know where you fit in the scheme of things before you give up a dream job/opportunity.
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Two body problem
in the classic sense refers to couples who both pursue academic careers. That is not at hand, yet. One of you is still a student. Commuter relationships are common amongst those with this problem, which is related to academic hiring. A couple in the same field is the most challenging of 2 body problems.
With a 2 body problem, love almost always involves a period of separation.
I have to disagree with most of what Cary said, since the question was framed in relationship to the '2 body problem', even if there isn't one yet. You have to have a commitment to have the problem, and this question is about making a commitment by diffusing the problem.
The girlfriend may not understand this conflict, as her mother folded to it. There was no negotiation, just a sacrifice for the more substantial career/talent. A mature young woman with some relationship experience and an understanding of the two body problem would never see this postdoc circumstance as an obstacle, but as a stepping stone.
I won't bother to explain in detail, but without reservation can say Take the Postdoc. Postdocs are invariably temporary and if your girlfriend is as serious about her research/career as she professes to be, she would do the same in a heartbeat.
Ask yourself this question: Did I pursue a doctorate to follow someone else's career?
Also, unless you are at a equally prestigious program, her Berkeley PhD is going to be WAY more valuable than yours. Nothing you've written suggests you want to be the trailing spouse, and if she wants to role reverse her parents' marriage, I can see no better reason to head for the hills and fulfill your own ambitions. By all means have a good cry and if your relationship is a meaningful one, she will have a desire (and perhaps the ability) to sustain it.
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ps
"I feel like I might die if I have to tell her that I'm going to Toronto, that I don't love her enough to try to find something in the Bay Area."
But you did try to find a job there. This pointless guilt is a clear sign your thinking is dangerously muddled. Don't dramatize a fault you don't have.
Finish your dissertation. Take the job.
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The Reality of the Job Market
I'm a chemist - a recently laid off and unemployed chemist - and the job market for chemists is brutal right now. Unless you are extremely lucky, this is a problem you're going to be facing throughout your career. You'll be laid off. She'll be laid off. At some point, you may both face the problem of having to relocate to find jobs. It's the reality of the job market for chemists.
I don't want to say "ignore love". Maybe love is worth sacrifice. But if you want to have a long-term career in chemistry, you will need a strong foundation. The right postdoc, where you can get strong references and make good contacts, is essential. That may mean Toronto, or it may not. There are certainly options in the Bay Area (it's not as if she's moving to the middle of nowhere.) But the decisions you make about your career now are going to affect you for years to come. If you stay in your field, people will still be asking you where you did your postdoc when you're 50.
You need to discuss this with your girlfriend. Even if you decide to go to SF with her, it's an issue that will probably come up again later (maybe when she graduates and starts looking for a postdoc). Lots of two-scientist couples have the same issues, and there's no one answer - but you have to talk it over and decide what you want to do and what sacrifices both of you are willing to make.
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Life, Or Something Like It
This is what I'd like to say to the LW:
My dear, young man: You are only 27. While your feelings toward this woman are undoubtedly sincere, you have so much time to establish yourself and take opportunities when and where the doors open.
I think you'd be foolish not to take the job in Toronto. Listen to what you said (I paraphrase): "It would be a perfect fit, if only I didn't have a girlfriend." Thing is, you don't really know for how long she'd be your girlfriend (I'm not doubting her sincerity either--it's all about youth and the nature of relationships).
You are not married. That would, frankly, put a different spin on things. But, since you're not, she should understand that this is a rare opportunity, and you ought not to deprive yourself of finding out if it can boost your lifelong career.
You have no wife, no children. Again, you're only 27. This is not the time to make sacrifices that can affect your whole life. You have the freedom and opporunity to pursue your talents, interests, and skills. You can establish yourself that way first, make yourself more marketable, and then see about job opportunities where she's geographically located (if you two are still interested in each other).
By following through on your career goals, you can actually become a more responsible, reliable person. One who will make a good life partner, maybe husband, if that's what you'd like. A man who thinks things through without being impulsive, who is preparing himself for the long run (which, as stated, can include partner, spouse, children, whatever you'd like).
Stick to your career goals for now, and the rest will follow. You have so much time and golden opportunity--don't set yourself up for regrets and potentially blaming someone else for what might have been.
There are some who might think I'm a real fuddy-duddy for this "think with your head, not your heart" schpiel, but not many people get such an education, degrees, careers. It's clear that you're deterimined to follow a certain career path.
Think clearly. You have only one body, one head, one heart, one future. Use them wisely. Time is on your side.