While studying for the CRM certification exams, I came across this MSDN page that very clearly says:
“Use jQuery with HTML web resources. We recommend that you use jQuery together with HTML web resources to provide user interfaces because it is an excellent cross-browser library.
With HTML web resources, you control the libraries that are present and there is no restriction against manipulating the DOM. Feel free to use jQuery within your HTML Web resources.
Avoid using jQuery with form scripts or ribbon commands. We do not recommend using jQuery in form scripts and ribbon commands.”
I have been working with CRM for quite a few years for now, and I have seen many implementations, the majority of which use JQuery everywhere.
For customizing forms, try the library SDK.REST.js . It is found in the CRM SDK and can be download here: