If you find yourself tweaking HTML to accommodate jQuery, you are probably doing something wrong. The selcctors are powerful enough to handle anything. $("input[name='whatever']") or $(".someWrapper input[type='checkbox']") for example won't care about the labels, and if you need to for some reason, you can walk back up with parent(s) or closest or whatever.

If anything the wrapping labels offer more flexibility because every level of tag isolation/lineage gives a chance for enhanced CSS that still requires dummy tags in most browsers (double backgrounds, e.g.).