Hi Wouter,
I think some support has been introduced for qualitative traits as well from version 2.4 onwards, but the description has not been updated.
The original website of the package is not accessible anymore, but please take a look at this archived version,
where you can find the updated description, which says, "Loki was originally designed for linkage analysis of quantitative traits, though there is some limited support for qualitative trait linkage analysis."
Loki is not being maintained by the original authors anymore, but you might find some information in the manual here:
@debian-med Should we patch the readme to include the updated description?
Regards,
Pranav