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.
My preference is to avoid jQuery completely. It's almost always overkill to use, it has some bad UI concepts in it, but because they are provided, people seems to want to use them (adding slow animations everywhere, just because animations are cool??), readability of the code is a problem (who came up with the idea that writing everything as short as possible would be a good plan?), backwards compatibility, both between jquery versions and gracefull degradation for browsers without javascript) is a big problem, and of course there are the collisions with other jquery instances as soon as your site becomes a little more complex.
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)