I'm not familiar with the details of certificate use, but as far as the cryptologic component there seems to be a reasonable fix, that will not require any change from end-users or invalidate existing certificates (apart from changing the hash).

The attack is based on finding a hash collision between certificates A and B, having the CA signing A, and using the signature for B. If the CA were to make a small change to A before signing it the attack would be foiled, since it requires active participation from the CA.

Suppose the CA started to add a few random bits to each certificate before signing it. The applicant is told what these bits are, so that they can use the signed (modified) certificate to verify themselves to users. With just a few extra bits this would make the attack unfeasible. Does this make sense?