How do I wrap the label text of a checkbox with a span tag?
You would either need to override theme_form_element in your theme, or, do a hook_form_alter, target specific checkbox form elements, and change their #theme_wrappers callback to your own theme implementation.

I personally would do the latter, since overriding theme_form_element will change the default rendering for any form element in your theme, and that may not be desirable in every scenario.