Considering ψ(x,t) to be a function, we expand it in plane waves,
ψ(x,t) = ∫√(m/E) (upexpi(p·x-ωt) + vpexpi(p·x-ωt)) d3p
The normalization is ∫ψ(x,t)ψ(x,t) d3x = ∫ (upup - vpvp) d3p
and as you point out this is not positive definite, due to the "negative energy states" v.
In the second quantized version u and v become operators which obey anticommutation relations. But even so, if you interpret u and v as annihilation operators the theory has negative energy states and an indefinite norm.
The solution is to reinterpret v as a creation operator: vk = wk. Then vpvp ≡ wpwp = 1 - wpwp and the norm is
∫ψ(x,t)ψ(x,t) d3x = ∫ (upup + wpwp) d3p - ∫1 d3p
The infinite negative part is discarded, leaving us with a positive definite norm.