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Not because of the moral equation (I join your comments on that--though I will further note that domestic partnerships were the leading edge of the movement at the time, and marriage itself was not really even then being seriously considered in the mainstream). But because the calculus was clearly wrong.
I too was worried about losing, and Dole was a credible, if uninspiring candidate. And the wipeout in the 1994 midterms (coupled with a long memory of losing, and a minority win in 1992) kept me worried. But it became--and should have been at the time--clear that Clinton was not going to lose that election. His 8+ point win was still the result of playing a prevent defense, and he could have stretched that to 10-12 points if he had really pushed at the end. Even if vetoing DOMA would have cost us 5 points, he could still end up winning by nearly the same margin if he had put some steam behind his campaign rather than coasting until the end.
Of course, it is a moot point--George W. Bush would have signed DOMA in January 2001.