I've sort of come to the conclusion that it is too important to both gay couples and secular couples that their relationship be called a marriage than to support the "everyone has a civil union" solution to the issue. I used to support that . . . marriage is religious, and civil unions are secular. But the word matters. For that matter, when Mike and I get married next year, it will be before a judge . . . and what we will be doing is getting married, not "getting unioned."
Nor can the government completely get out of the marriage business. Marriage is partially a contract, carrying major legal obligations. Even if we abolished joint tax filing, there are many, many reasons to have marriages legally recognized . . . and that means the government (at some level) can't get out of the business entirely.
I've come to the conclusion that the government should just call them all marriages. If a religion doesn't want to marry a couple, or doesn't want to recognize a marriage, that is absolutely their prerogative (we have religious freedom here! Just like if a religion wants to recognize multiple marriages, they should be free to do so, but the government shouldn't have to . . but that's a whole other discussion), but the government needs to recognize all marriages that are lawfully registered with it equally as "marriages." Its the only fair solution. If you find the fact the government lets gay people get married, then just say to yourself and your kids, "We don't believe that those are real marriages, because yadda yadda . . ." Heck the Catholics have done it for years with people getting remarried (secularly, or in another church) after a having a divorce.
Edit: Renee is right that you could just designate things instead of having formal marriage recognition. My concern there is that it by and large wouldn't happen consistently. People wouldn't understand, and wouldn't get around to, the paperwork, wouldn't know everything they had to do. Lawyers would clean up selling "marriage packages."
The convenient thing about marriage, from a public interest standpoint, is that it provides a set of defaults . . . you get married and this, this, and this, happen automatically. That can be a problem in its own right, of course, but it makes things a whole lot simpler, both for the courts (which have to settle any disputes) and for the couple themselves.