There are two things here to consider: One, the Biblical teaching of women in the church and two, what our responsibility is to the church we attend.
As for the Biblical teaching of women in the church, I know well 1 Timothy 2:12 and 1 Corinthians 11. Yes, these passages seem extremely straightforward in saying that women are not to speak out in church or to hold any kind of authorative position. However, this is a place where I've been challenged in the past 8 years or so to rethink, and to separate what very well be a tradition of men from the whole of the Word of God. And, it's a study that I've tried to share here as well as on other forums and find that usually one gets hit with 1 Timiothy 2:12 and 1 Corinthians 11 & 14 and that's it, end of story, let's all just stop thinking and regurgitate what's been pounded (by men) from the pulpits, for 1000+ years. ;-) It's amazing that I have found biblical teachers and scholars who despise the use of 'proof texts' and yet, when this issue comes up, out pop these texts and poof, the matter is to be considered settled. Well, I have a real problem with 'proof texts' as well, and when one diligently studies the issue of women in the church, it's not quite as black and white.
The second issue should not to be dismissed lightly though. As you say, its not unusual at all to not suscribe fully to all the teachings of one's church. However, it's my opinion that if one is going to become a member of a church, then, in the interest of church unity, one shouldn't fight too stringently against the teachings, unless the teachings are out and out wrong. Even then, if after sharing a Biblical point-of-view, and listening to the church's stand on it, if one feels very strongly about the issue, it's probably better to seek a church which teaches that truth, rather than be divisive. Again, this isn't in matters of wrong doctrine, just doctrines that we, as Christians, can have legitimate differences of opinion over.
As of now, due solely to wifely submission, I'm attending a church in which I don't necessarily agree with several points of doctrine. In the case of my church, what is the issue for me is liberal theology. We had an interesting time in Sunday School just this week, when the pastor danced around the issue of Biblical inerrancy. I think the thing is, she (yes, the pastor is a she) believes in Biblical inerrancy, but the denomination doesn't.
Because my husband wants to go to this church, it is the denomination he grew up in and his family are very faithful members of the church, I go to it. And, I'm not going to be divisive either. One thing about it, we can dialog in the church fairly easy and I can give my views, but I'm not going to be divisive. In these areas of legitimate disagreement, the whole idea of 'agree to disagree', while lousy theology is simply the best way to move forward. Church unity is a very important issue.
I would very much like to discuss the issue of the biblical position of women, but before we plunge into it, Jules, I do see your dilemma, it's one I struggle with myself (although the opposite is true of our church, they go to extreme liberalism), and all I can say is, if you are committed to staying with your boyfriend in anticipation of getting married, then this will most likely become an issue of wifely submission for you as well, and you'll need to decide if this is something that's a "deal breaker" before marriage. Because, once you marry, then wifely submission does come in. However much one can (at least try) to discuss the position of women in the church, the position of the godly wife in the home is one of submission (not subservience, two different things there) to her husband. It's a big decision and with lots of ramifications, and the idea of not being unequally yoked comes into play here.