I agree with @agramfort --- changing this line will break code ...
In Epochs and Evoked we will need to make this behaviour dependent on the availability of comps. E.g. don't pick refs if comps are empty and so forth. Then we need to check that refs aren't treated as data channels by our viz routines and so forth.
I would give the advice not merge any change that is intended to address this issue without extensive trying / testing with CTF KIT BTI datasets.