As someone who does application security assessments for a living, the biggest problem with jQuery is the lingering, outdated, vulnerable versions that are pervasive (1.x and 2.x in particular) in so many applications. I don't care if you decide to use jQuery or not, just have a plan to maintain it and be able to update it without breaking everything, should the need arise.
If you allow unchecked data to be stored & retrieved there are some XSS vulns in older versions. Ideally this would be prevented in a sane environment.
/preaching