Merge without marking conflicts in working tree

Is there a way to do a merge but only record conflicts in the index, not update the working versions of files with conflict markers?

Like many people, I use git to manage configuration files for my shell, editor, git itself, and a number of other things. The vast majority of times that I update things no conflicts are occur and everything just works, so I'd like to avoid extra work in this case. But occasionally a conflict will occur, and if it's in a file that will be read while trying to resolve the conflict this can make things more difficult.

I'd like to find a way to have the conflict recorded in just the index without touching the working tree. I could then use my usual tools to resolve the conflict without the errors caused by the conflict markers. I generally use vim+fugitive to resolve conflicts anyway, and typically the first step I take is to replace the working-tree version with the merge-base version, completely ignoring any conflict markers.

If there isn't currently a way to do this, I was thinking of implementing something like an "ours" value for merge.conflictstyle configuration.