I believe in nature being the best way too, and yeah the mum of lots of species seem to just know when something isn't right and either end it .. or like in your case, dispose of it because she just knew ....
as to the spread out birthing thing... i was told recently ( admittedly i didn't know the person from Adam so i cant garentee the source) that if you wanted a small litter leave the jill in with the hob for 24 hours, 3 days for a bigger litter etc... IF this is so... could it be possible for different times of gestation? ie.. the first kit was born of the first coupling, the next bun