I always took the Steel Vipers' lack of participation in the Great Refusal to be them sitting it out, than outright siding with the Wardens.
Remember that at the time of the Great Refusal in April 3060, the Vipers had just endured some pretty nasty internal strife two years earlier centered around the botched attempt by saKhan Christopher Ahmed, a Warden, to advance that cause during the Refusal War. The revelation of Ahmed's actions, his trial, and his subsequent death at Andrews' hands gave both the Crusader faction and the remaining Wardens among the Vipers lots of reason to be angry at each other.
From Sarna, by way of Field Manual Warden Clans:
The trial of Christopher Ahmed caused great anger among many of his supporters though, and for the next few months the Steel Vipers were paralyzed by political infighting
With Ahmed went a great deal of the Warden political clout within his Clan, allowing the Steel Vipers to shift toward a more Crusader-like path than ever before, while still espousing the vision of Sanra Mercer.
Plus, the Vipers were in a rebuilding/restaging phase after suffering some losses in the Harvest Trials following the Refusal War and, more importantly, gearing up for their attack on the Jade Falcon Occupation Zone in 3061.
Coming off a major internal issue and with their own major military campaign imminent, it's not hard to imagine that Zalman and Andrews were willing to side with the Wardens by default rather than by active choice. Given that one of Andrews' first actions as ilKhan was to put the repudiation of the Great Refusal to a final vote, I always figured his and Zalman's votes in 3060 were just them playing the long game--"we're not going to stand by this anyway, but why be bound by it if the Crusaders lose?"
As far as Andrews having a change of heart, remember that the Vipers are Mercer-first, Warden/Crusader second, so someone like Andrews could (and did) rise to power along those lines, and could probably excuse his having voted to not participate in the Great Refusal and calling for its repudiation through that lens.
