It is essential in accurate research to have both pieces of information a standard spelling for locating purposes and the exact spelling used in a particular document.

I would propose the following compromise:

Enter the standard spelling of the name, so that a search of the database files for that name would be sure to find it. But I also enter the exact spelling used in the original record into the notes referencing that person or event. Also, PAF (as well as others) have a place to enter "also known as" names.

While there is no method for the mass changing of all surnames to make them consistent, there are methods for ensuring consistency as the names are originally entered.