I have debated on making this an official answer. But there are a lot of little points you have to consider.
First, the direct answer to your question:
Should I bring this topic up during the interview, or should I avoid discussing it? I don't want it to look like I'm having a problem with them, even before I'm hired.
YES!!! The company made a deal about talking about their religious beliefs. You need to know, if your going to be comfortable working there. Remember that the interview as also about you interviewing them. If this is an area for possible concern for you, then mention it, ask, and investigate. Be polite, but don't be afraid to be direct.
You have hit on one of great american paradoxes. As a nation we strive for religious freedom and tolerance, but some religions actively work against religious freedom and tolerance. It is a big web of gray areas. How can we be tolerant of of religion if that religion is not tolerant of other religious beliefs? There is no easy answer for this. There are laws and what not, but it's never cut and dry. Most people adopt a live and let live type of policy, but that doesn't mean everyone does. And to be honest, that's fine too. This brushes up against a very complicated topic. You need to ask questions and figure out of the culture there is one that you would feel comfortable in.
This gets to be a gray area as well. There are laws against discrimination for religious affiliation, but there not as straight forward as people would have you think. Because religion is a very fundamental decision in ones life, it can be difficult or impossible to differentiate between I don't like this person from I don't like this person's beliefs. Do not think that the law provides you with a blanket anti-discrimination shield. It doesn't. The owners, and other employees rights to work and practice their religious beliefs are also taken into consideration. It gets very tangled and very complicated. It's rarely cut in dry in this area.
In the US We have a concept that a company is it's own entity. Usually, that company has a set statement of beliefs (or goals), and the workers in that company are expected to make decisions "on behalf" of the company that support that view. Even if a company is your life's work, the normal thing would be to treat that company as a separate entity from your self, and make decisions separate from your own point of view. That being said, it's not unusual that the owner(s) of a company apply their beliefs to the company. For example Chick-fil-a is not open on Sundays because the owner believes in having a day off for family time and religious worship.
First and foremost you need to figure out if your going to be comfortable working there. If your not, then you should look elsewhere for employment. You can do this by asking questions in the interview and stating your position and judging their reaction.
Second you need to understand that the law is not going to help in this case. You would, at this point, have to jump through too many hoops to make any kind of a case. This would likely tie up your situation for years to come, and in the US make a giant red flag when looking for other work (no one want's to hire any one that is part of an ongoing discrimination case, and in most cases, don't want to be any part of one that happened in the past).
Third, understand that they have the right to "run their company their way" and while you may be able to go to court and win a something or other kind of judgement against the company, that won't change the fact that it's "Their" company and "they can run it there way or not at all!!!" if that's the kind of stance they take.
Mostly understand that in the US, it's perfectly acceptable to have a religious belief, to apply those beliefs to your company, and have the company act on them. It's not ok to penalize someone when their beliefs differ from your's or your company's. At the same time, it's not as simple as black and white, and there are many, many shades of gray.