since your html 5 is going to sit inside a webresouce or an iframe, all that applies here is how far your browser supports the page.
not quite sure what you mean by integrate, can you please elaborate? If it is getting data/sending data, you could use platform service.
for example, XrmServiceToolkit uses jQuery and never had an issue.
CRM natively uses JQuery (saw some js files to that effect.)
please let us know.
regards
Jithesh