There are, on a philosophical level, significant clashes between the agile paradigm and Quality Systems such as ISO 9000 or CMM/CMMi, this is already presented in the Agile Manifesto. Agile Development is based on what I would call post-modern paradigms when compared to the plan-driven and early iterative development methodologies which are based on a positivist paradigm.
The underlying philosophical challenges cannot be easily mitigated. But a purist agile paradigm may tend to stress a positivist paradigm as well and this can be dangerous since then agile would not be agile any longer.
While it may not be possible to completely remove the challenges between agile and quality systems, it is possible to learn to live with some tension between different paradigms.
There are some obvious areas of conflict, for examplethe Agile methodologies strongly discourages unnecessary documentation, and questions that it is possible to provide all requirements up-front. ISO 9000 on the other hand demands requirements up-front and documented evidence of almost anything, but such practical aspects can actually be mitigated with relative ease. Other aspects may demand much more effort. In particular the internal auditing process is problematic and other means of ensuring compliance may have to be considered.
We have in my company systematically piloted a number of organisational changes in order to better support agile development. We have done this within the overall framework of our ISO 9000 system which is used a structure anda a gatekeeper. To do this we have used Action Research, which in it self is a kind of agile methodology, although of much older date than agile development.
While the presentation has a strong theoretical foundation the focus is on the practical experiences we have had of building an organisational framework for agile development and while doing that suggesting a few means to mitigate the challenges mentioned initially.