Is it Ok in practice to rely only on the first 64 bits of a scrypt hash in this scenario?
No, you cannot assume that no collisions can be found if there is a chance of $1 \over 2^{32}$ per try. That's too high a risk for almost any kind of cryptographic scheme, especially if parallel attacks are possible. This is true by definition for scrypt as you can simply try multiple passwords at the same time. That kind of parallelization cannot be avoided even if you modify scrypt.