Well I think there are as many views on this one as there are sheep-keeping and vets... Here's mine and his.
If you cannot operate a closed flock then you want to be breeding for footrot resistance. If you operate a closed flock you can maybe try for eradicating the disease. It ain't easy - I suspect it's easier done where ground and climate are less wet than ours, too.
The downside of eradicating the disease from your farm is that if ever the germs do arrive, then unless you are vaccinating for footrot annually, the bulk of your flock will get an infection - and may have very little immunity or resistance to it. Hence why I say don't go this route unless you have a closed flock.
To breed for footrot resistance, don't cull the first time she has footrot. Treat it if you have to (some of them overcome a light dose without any or much treatment, most of ours will recover with a trim and some terramycin spray at most - and if you are trying to engender resistance, you don't want to be using antibiotic injections if you can avoid it) but if she comes down with it again, cull her.
Of course ewes which never get the disease in the first place are more resistant than those which need an infection to become resistant and ideally you'd have more of the first than the second.