Beating with rank 100 basically just gives you a short bonus movie after the game has ended, so you can safely complete the game to 100% and then finish it as normal. You'll still get to see the normal ending and
the bonus movie.
It's a short video though, and definitely just a little bonus for those determined enough to get rank 100. If it's going to take you ages and ages to do it I wouldn't bother. It's not really meant to be something you know about until you get it.