That is the worst solution of all. It means that you will always miss out on one route, no matter how you choose. One of the main draws of harem games is that you're not forced to drop one route for another, that you can have all the girls and all the events if you want.
It's also the least flexible model of all. If you have events ABCD, then making A and C mutually exclusive allows only ABD and ACD paths, whereas optional routes allow AD, ABD, ACD, and ABCD.