Hi,
I am not sure how you are going about using IronPython. I have been using Python for pretty much all my input and output from DHI MIKE. You just have to proceed in same way as using Matlab Toolbox, You will need to use the .dll files which are read by IronPython or Python for .NET toolkit. It allows you to use the DHI toolbox. I have been writing a set of scripts for the same process, though i can't share my scripts, I would be more than happy to help you with the process if you give more details how you are doing it and at what stage are you getting problems.
Extracting and converting it to any other format is simple step once you figure out how to import the arrays from dfs2 files.