If you ask most people if they give punctuality grades they normally say no initially. But if you ask someone to finish the following statement:
"For every day the assignment is late...."
They usually will say 10% or a letter grade will be deducted. That is a punctuality grade (well penalty), plain and simple. As a school you need to ask:
1) Does this conflict with our primary purpose of grading?
2) Does it disproportionally affect certain groups of kids?
3) If it is important (and it is), could we report it seperately from academic proficiency?