It’s been shown multiple times before that there’s no technological reason you can’t put someone in the buffer and take two out. Thomas and William are proof of this.
The Voyager crew likely had access to the records of the Thomas case, having happened a decade earlier. Though I admit I don’t know if the information would have been classified or withheld for some reason.
Assuming they had the information, they could have likely attempted a duplication, and unmerge one of the two resulting Tuvix’s.
I found myself so pissed off this wasn’t even considered during the episode. It’s like they just forgot duplication was a possibility, even if it wasn’t a super sure fire solution.