On a technical side, if you want to avoid cluttering your display formulas with punctuation in the LaTeX code, but still be able to show it inside the formula, take a look at this brilliant answer by Alexey on stackoverflow.
You may even later disable the display of that punctuation if you think that it gets in the way (which is my point of view), look at the comments to the answer linked above.
For me this is the perfect solution: I can send a paper with punctuation for publishing, or compile it without punctuation for me, and I can always copy-paste the display formulas without having to remove that pesky punctuation.
