I see this solution only as a temporary solve until a/the mk_apt can successfully filter this out.
Commenting apt conf and/or sources is from my point of view - as it is not under the control of CMK itself dangerous and can have unwanted side-effects on the monitored system.
Plus maybe in future updates this will be re-enabled, so the solution should be done in the plugin itself, not on the monitored system.
- Glowsome