That cross-over, how does that exactly work? In the Netherlands you can marry by law, and if you do that, you can also marry in a church.
The former is a legal thing. The latter could be seen as a spiritual thing, or a bigger thing, or whatever, but it does not prevent anyone out here to marry by law.
So, if a certain minister or priest or even a bishop is against gay marriage, that is his opinion but it does not prevent a parliament to change a law.
I am not aware of gay marriage in catholic churches but if a church is not forced to have the same weddings as in municipality buildings, it makes matters less complicated.
edit:
(extra info from wiki): After the Dutch parliament legalized same-sex marriage the Protestant Church in the Netherlands permitted individual congregations to decide whether or not to bless such relationships as a union of love and faith before God, and in practice many churches now conduct such ceremonies.
So, the churches were not forced, they chose themselves what to do.