When I do a merge conflict resolution with Kdiff3 (and other merge tool I tried) I noticed that on resolution a *.orig file is created. Is there a way for it to not create that extra file?

A possible solution from git config:

git config --global mergetool.keepBackup false

After performing a merge, the original file with conflict markers can be saved as a file with a .orig extension.
If this variable is set to false then this file is not preserved.
Defaults to true (i.e. keep the backup files).

The alternative being not adding or ignoring those files, as suggested in this gitguru article,

git mergetool saves the merge-conflict version of the file with a “.orig” suffix.
Make sure to delete it before adding and committing the merge or add *.orig to your .gitignore.

Berik suggests in the comments to use:

find . -name \*.orig 
find . -name \*.orig -delete

Charles Bailey advises in his answer to be aware of internal diff tool settings which could also generate those backup files, no matter what git settings are.

• kdiff3 has its own settings (see "Directory merge" in its manual).
• other tools like WinMerge can have their own backup file extension (WinMerge: .bak, as mentioned in its manual).

So you need to reset those settings as well.