There is a better way to phrase it, but it's also OK. That is to say, in contexts other than a commit message, you would probably want to rewrite the sentence, but for an internal note, it's fine.

The main issue with the sentence is that you're using commented out as a compound adjective and so you should probably hyphenate the phrase: "Remove the commented-out code." Hyphenation would also improve your last example sentence: "Help the left-behind people" is better, but "Help the people who were left behind" is better still.

If I were trying to express the idea of your commit message in a more formal context, a context where prose style is important, or really any context without a strict and low character limit, I would write, "Remove the code which was commented out."