1) I think the implications you speak of were merely fears, and most people that I heard did not believe that churches would actually be required to wed same-sex couples. (Although perhaps required is the wrong word, as I believe the worry was that they could lose their tax-exempt status if they don't, but would still be allowed to continue as churches following their own beliefs.) Massachusetts has had same sex marriage for years. As far as I know they haven't forced churches to marry same-sex couples there.
2) At the time of Prop 8, same-sex marriages were allowed in California. If the writers of prop 8 were concerned with preventing churches from being required to wed same sex couples, they could have written an amendment that reserved the rights of churches to marry whomever they choose. They did not do that, they wrote the amendment to revoke the right to marriage that gays had at that time.
3) Civil unions versus marriage is an interesting side discussion, but basically you end up with the separate but (not-so-)equal problem. I guess if one is concerned that allowing same sex marriages would lead to churches having to perform them, then that distinction might be relevant, but otherwise I don't see any reason to use different terminology for the two types of unions.
4) Separate from the issues you mentioned above, I wonder whether the imposition of the values of a certain religious group (those that don't allow same sex marriage) doesn't infringe upon the values of other religious groups (those that do allow same sex marriages). How can one claim that allowing same sex marriage infringes upon their religious freedom, without acknowledging that disallowing them would infringe upon the religious freedoms of others?