Your translation is quite good! I don't think I would use both sed and etiam here; etiam on its own seems sufficient. And it typically comes second in the clause. So I would say:
Tempus fugit; muscae etiam fugiunt
However…
The pun, unfortunately, doesn't work in Latin. The verb fugere means to flee or run away, the noun musca means the insect, and the verb volāre means to move through the air. None of the three words are related or look particularly similar. (The translation above assumes that the flies are running away, e.g. from a flyswatter; if you want to say that flies move through the air, you would need volant.)