To remove code tags, check out PHP's strip_tags function.
http://us3.php.net/manual/en/function.strip-tags.php

You can easily parse or split text based on Returns ("\n"), but you are right, if the user does not hit Return, the text will wrap to another line in the textarea, but is actually not a seperate line. All you can do at that point, is break the string into "lines" based on character length. For example, you may figure that about 60 characters make up a line. You could then split the string into 60 character sections. You can even add logic to prevent splitting mid-word. But you still will not have a way to split the string exactly as it appeared in the textarea.

If you really must have this, you may have to use multiple text inputs instead of a textarea. (One text input per line.) This may or may not be an option in your case.