It's not merely that "the structure of checkboxes changes" -- rearranging the original DOM elements in a Marketo form is largely harmless and we do do it all the time -- it's that this particular plugin completely removes the existing checkbox elements from the DOM and inserts new elements. That leaves the form in a partially-broken, partially-working state (and therefore broken in practice).
This plugin is clearly not designed to be integrated into an existing forms JS library. A Marketo-savvy JS developer would be necessary to make this work. There may be other libraries that don't require such work, as they're more sensitive to complex forms environments and don't expect a plain vanilla HTML form.