One way would be to use the Perl rename utility. The Perl regex .(?=.*.) matches a dot only when there is another dot later.

rename 's/.(?=.*.)/ /g' *.*.*

If you want to act on files in subdirectories as well:

shopt -s globstar    # you can put this in your ~/.bashrc

rename 's/.(?=.*.)/ /g' **/*.*.*

This works assuming you don't have dots in your directory names. Otherwise I think the simplest method would be to use find:

find -depth -name '*.*.*' -exec rename 's/.(?=.*.)/ /g' {} +

Alternatively, using zsh (this only renames regular files and leaves directory names alone, due to the glob qualifier (.) at the end):

autoload zmv    # you can put this in your ~/.zshrc

zmv -Q '(**/)(*.*)(.[^.]##)(.)' '$1${2//./ }$3'