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.
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.
Because negative pion is not known hero of strong and weak interaction.
Brefly - in 1932-1934 James Chadwick which knew no negative particle except for electron, told to physical community that neutron cannot be composite particle consisting of proton and electron. From this obvios fact he made speculative statment that in this case neutron is elementary particle like proton. Though it is not logical, physical community believes it very much after almost 100 years.
That makes impossible to understang real role of negative pion in weak and strong interaction. As well that belief makes impossible to understand that proton and negative pion compose atomic nuclei. And neutron is just composite of proton and negative pion.
As well it makes impossible to understand that negative pion inside neutron and atomic nuclei is responsible for beta-decay.
You look at most important particle from the point of view of nucleus when you ask about negative pion beta-decay. Although electronic (not muonic) pathway is most important. As negative pion inside nucleus cannot decay to muon - binding energy of negative pion to protons is bigger that energy of muonic pathway. Electonic pathway gave energy enoph to be favorable for neutron and some nuclei.
