So it seems that's currently not possible. The closest thing to disabling
conda would be providing you're own job_conf.xml.
A flag like --no_conda_dependency_resolution analogous to --no_conda_auto_install would be nice.
Usecase is if you're developing a python package, and you would like to test it with planemo before packing it up in pypi followed by creating a conda package from pypi.
You can also work around it by removing the conda package or the requirements tag, but it would still be nice if planemo could be used in that scenario.