When doing a google search to see of the following combination: agnostic, catholic, marriage (I was looking for tips and suggestions to create a balanced ceremony) most of what came up in that search was a great deal of angst about whether an agnostic and a Catholic can actually wed.
Given that I am currently working through my own angst on the issue, I feel like this might be something that I need to consider trying to answer.
I don't have a solid answer for this question because I struggle with it continuously in terms of my own marriage. I can only answer from my perspective and personal experiences. Given how liberal both my partner and I both are and the amount of problems that we still end up facing as we plan a wedding, I don't know that the decision is for everyone.
Before you start thinking that I'm saying break up with your partner, let me clarify: It can be done, it just requires a LOT of compromise, negotiation, and constant communication. It really depends on the couple, how much they want to make it work, how well they work together, and their ability to navigate some rather thorny issues.
For example, I don't believe in the Bible. I just don't. I feel that there are many important life lessons in it and that it is an amazing sociological record of the cultural values of a specific group of individuals in history (which doesn't lessen it's worth), but I don't accept that it is without error. For me the Bible was written by men, at a specific time, with specific agendas and values, for men. Academically, the text is very flawed and full of inconsistencies that have been interpreted and manipulated far too much throughout the course of history. My partner knows this, accepts it, and to some extent, agrees with me. This is important for us as a couple because many of my value systems and his end up being aligned and negotiable because of this. If he took everything in the Bible literally, we wouldn't work. Our views would be too oppositional and there would be no way of reconciling our differences. For another couple this might not be an issue, but for me it is, and by extension becomes a core issue between making it work between the 2 of us.
It is VERY important to him that any children we may have, be baptised. I am ok with doing this provided that they be raised with an awareness of other religions and their merits, or more specifically, with the ability to question religion and explore their spirituality in the ways they need to. If I wasn't willing to negotiate baptism and confirmation, he wouldn't be ok with building a life with me.
I think that a couple with different religious identities can work, but each member of the couple has to be flexible in terms of what their religion means to them and in their acceptance of other beliefs. Personally, I don't think we would have ever worked out if the boy had been a staunch Catholic and I a devout Atheist. My faith that there is something out there and constant search to find it, and his acceptance of other ways of finding God have made all the difference in our relationship. We wouldn't work without them.
The ironies of all ironies behind how we make it work:
Despite my being more liberal in my religious views, he is more flexible in his acceptance of our different paths. Even though I am compromising more in terms of our wedding, he is compromising more in terms of our marriage. I end up navigating the tricky conservative value systems in his family, but he is the one that is changing his relationship with them.
That said, wedding planning has still caused a great deal of turmoil in our relationship as we navigate community, family, and friend expectations. I have compromised a great deal by agreeing to marry within the Catholic church (I can't even begin to emphasize how much in terms of my own beliefs) and he has compromised a great deal by agreeing to marry in a Catholic church that isn't his own in order to find a priest that I felt comfortable with marrying us. I have received an untold amount of flack for compromising my values (gay rights, pro-choice, feminism) and he has experience unending pressure from his parents, family, and religious community for not marrying in his church.
I won't lie, it hasn't been easy. Coming from someone fighting this battle, if your values are non-negotiable and your faith of utmost importance to you, make sure you have these conversations before getting engaged. Figure out what you are willing to negotiate and where your boundaries are before agreeing to spend the rest of your life together.
Because trust me, once family and wedding expectations are involved, it only gets more complicated!