Well, its not technically managing conflicts with submodules (ie: keep this but not that), but I found a way to continue working...and all I had to do was pay attention to my git status
output and reset the submodules:
git reset HEAD subby
git commit
That would reset the submodule to the pre-pull commit. Which in this case is exactly what I wanted. And in other cases where I need the changes applied to the submodule, I'll handle those with the standard submodule workflows (checkout master, pull down the desired tag, etc).