As with other issues which can arise in a relationship, it all depends on how you are both prepared to work around it. Differences in religious belief are not themselves deal-breakers - the Deputy Prime Minister of the UK at the moment, Nick Clegg, is an atheist yet he is married to a Catholic and they are bringing up their children as Catholics. It all depends on how the individual couple approaches it, and as Jess has said if you're still together 5 years down the line and still discussing a future together then that would suggest it's something you can work around. On the subject of the Catholic wedding, there are two types of ceremony - one with the Eucharist and one without - so again there's potential room for manoeuvre on that if and when it becomes an issue.
Hope that helps.