I've experienced an other problem with jquery and DNN:
I've build a module which uses jQuery. It can't include it's own jQuery as it collides with DNN's. So I don't include jQuery and use the one DNN already includes.
There are 3 problems with that approach:
1) DNN 7.0 used a pretty old version of jQuery. They recently (DNN7.1) included a newer jQuery, which was a huge jump in jQuery version and because the people at jQuery don't seem to care much about backwards compatibility, this broke a lot.
2) I can't upgrade DNN without the risk of having to upgrade my module also. Uncontrolled jquery upgrades aren't fun.
3) When DNN doesn't use jQuery itself (for example when popups are disabled) it doesn't include jQuery either, again breaking my module.
I did save some time building the initial module, but I've spent way more time on fixing jquery issues ever since (and I've still not fixed them all)