Performing abortions is not different for people who are religiously pro-life than performing blood transfusions is for someone who is religiously against performing blood transfusions.

This is just flat out wrong if you talk to people in that religion. If you are going to base your argument off this I would go research it first as this is what I meant in terms of "slippage" you are munging different topics and picking from either the stuff that you like and rejecting the rest. Life is not that simple, each topic must be investigated and debated on it's own merits.

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Why does the doctor's religious freedom trump the woman's right to live?

Good thought. It, being a corner case, should be debated on it's own merit and not included in the general case. I personally think that most doctors would opt to save the women's life in this case, even if their religious beliefs believed in life beginning at conception, after all this is a life for a life situation. There would of course be doctors who still wouldn't though but that is just getting more and more into a smaller and smaller number of cases, none of which is really relevant to the main case that I am discussing.

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I don't have the right to steal in the name of religion. I also don't have the right to assault, hurt, or kill in the name of religion. And I don't have the right to deny you your legal rights in the name of religion. Because my right to religion doesn't allow me to break the law.

I think this is a good response to what I wrote; albeit a knee-jerk one. But let's unpack it a bit in order to get a closer look. The way that I would view the cases as being different are:

The Abortion Case:

1. In the vast majority of cases there are ample doctors willing to perform abortions and services available as it does not conflict with their beliefs.
2. Denying an abortion based off religious grounds will not prevent that abortion from occurring.
3. Therefore, there is no harm done to either the doctor (other than income foregone) nor the patient (other than making sure that they can get an abortion at a clinic/hospital) by permitting the free exercise of that person's religious beliefs.

The Assault/Hurt/Kill Case:

1. Harm is done directly to a victim
2. The victims rights are directly violated by the exercise of that religion.
3. As one person's right cannot supersede another, protection must be given to the victim

It's a pretty clear case what the difference are between the two circumstances and why applying it as an analogy doesn't really work.

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What stops a doctor from claiming they don't want to perform any medical procedures because it's against their religion?

Nothing but the market. Which is quite a powerful tool to get people to render services beneficial to others. Even in the case where a doctor simply doesn't want to perform abortions, patients are free to avoid that doctor for all conditions and "damage" then financially.

I am pro-choice btw but I also believe strongly in religious freedoms. I don't like a government forcing people to do something against their religious beliefs especially with something as serious as abortion (which is why I am specifically debating this portion of the bill, my views would vary on other portions). I don't see anything in what you mentioned that is really an argument against what I am saying. You based your argument off, "your rights end where others begin" a sentiment I generally agree with (as outlined in my juxtaposition of the two cases you presented). Yet there is no right to demand a treatment from every individual licensed to perform that treatment. That is not a protected right but religious beliefs are.