Adding a time penalty such as 30s will mean that the fastest guys can probably afford to skip 1 or 2 controls and still comfortably qualify.
Do you not think it defeats the point of sporting competition if you are able to finish (potentially with a good result) without having met the requirements of completing the sporting task?
This approach seems to be perfectly acceptable in biathlon - miss the target and effectively incur a time penalty by having to ski the additional loop.