So you're at an impasse. If you can't overcome it, you SHOULDN'T get married because frankly, choosing the church you get married in is the easiest part of working out an interfaith marriage.
If you REALLY want to make this work, then the two of you, as a couple, should take a class about Catholicism (it's called RCIA and it's free at her church) and then also take a class about your religion, if one exists. If not, perhaps your preacher can recommend some books that you can read together about the origins and beliefs of whatever kind of Baptist you are. When both of you have a comprehensive understanding about each other's religion, you will see what you have in common and you will be able to determine if this relationship can work.
Some things to keep in mind:
1. She wants to marry in the Catholic Church because Holy Matrimony is a sacrament for Catholics (like baptism, delivering grace to us from the Lord). It's not a sacrament for Baptists.
2. In the US, most couples marry in the bride's church.
3. If you do get married, she'll need dispensation to marry a non-Catholic, but that's easy to get.
4. She will have to make a solemn vow to raise the children Catholic. Since you aren't Catholic, you don't have to make this promise, however, you do have to agree to let her raise the kids Catholic and you have to promise to not prevent her from going to Mass and giving the kids their sacraments (Baptism, Confirmation, Communion, etc.). You can also teach them about the Baptist faith; you just can't work against Catholicism.
5. As a Catholic, your wife will want to (and be obligated to) uphold all the teachings of the Church, which includes not using birth control, being open to life, going to Mass every Sunday and other Holy Days, etc. She can also go to church with you (indeed, you should both go to both), but she can't receive Communion at your church when/if they have it, and you can't receive the Holy Eucharist in the Catholic Church.