The idea came to me whilst using Switcheroo
Using a similar interface
First row is the 'Target'
Second row the 'Replacement'
Drag Target file to 'Target'
Drag Replacement file to 'Replacement'
On running the Replacement file is renamed to the target and then moved to replace the target (though the sequence may be slightly different to avoid conflicts)
Mouse only operation:-
Advantage two file drag-drop, and run. Total 3 actions (4 if confirm is an option)
Two drag-drop, switch, select Replacement, rightclick, delete, confirm. Total 7 actions
Using Windows (7)
Select target file, select filename, rightclick copy filename, select Replacement file, select filename, paste filename, select Replacement, rightclick, copy Replacement file, select Target location, paste file, allow overwrite, select Replacement file, right click, delete, confirm Total 16 actions
If there is already something out there...