The program that 'creates' the 'unpunctuated messes' is your web browser. If the <br> tags aren't included then the HTML interpreter (your browser) keeps putting text on the same line until it reaches the width the particular window allows.
If your friend has a program that translates text to braille and it is not configurable to remove whitespace I suggest he get a new program. The coding to ignore specific text, blanks or html tags is trivial compared to the other things such a program would have to consider.
IBM has a Special Needs Department that deals with these kind of issues. Their homepage is at http://www.austin.ibm.com/sns/
For additional information call IBM Special Needs Systems:
(800) 426-4832 (Voice)
(800) 426-4833 (TDD)
or send email to: firstname.lastname@example.org