standard model - Pion Decay and Fractional electric Charge disappeared, why?

Since the charged pions decay into two particles, a muon and a muon neutrino Fractional electric Charge disappeared, why?

The decay proceeds by the weak interaction $W^{+}$ and can be visualized in terms of Feynman diagrams.

my suggestion is that the Fractional electric Charge disappeared because it does not exist at all in the Quarks mechanism.

Answer

As you say, there exists a Feynman diagram

for the process, and the real question is: "what happens with the quarks"

The up and antidown quarks manage to "annihilate" into a virtual W+ which decays into the mu+ and nu_mu.

Simple. All annihilations "disappear" some quantum numbers conserving the over all quantities.