How to protect against ephemeral key reuse in some signature schemes? Given that some signature schemes (for instance Elgamal) use an ephemeral key that cannot be reused ever. How do people usually protect against this?

I'll elaborate more: if you reuse the ephemeral key in Elgamal for two different signatures you have (AFAIK) effectively given away your secret key. If the same public/private key pairs are normally used for long periods of time (sometimes years), how can you be sure that you never repeat the ephemeral key? 

I know this key should be chosen randomly and given its length the probability of reuse is very tiny. But the risk is so big that I think it's worth taking some countermeasure. 

Is there any standard way of dealing with this or am I totally missing something?
Would you say: the probability of mass life extinction on earth caused by asteroid impact is like $2^{-28}$/year; but the risk is so big that I think it's worth taking some countermeasure?

The applied cryptographer's position is that below a certain probability, like $2^{-40}$ lower than mass life extinction on earth, there's no need to mitigate the risk. It is best to spend effort on countermeasures against a stuck TRNG, by accident or attack.