Personally, I don't like skaven, I find them by no means "cool", but rather unstylish in a fantasy setting, plus, they are Games Workshop stuff
But I like your idea, I always like quoting a classic, an killing off the skaven makes it even better
Is there a way to include the second half of the tale, too? You know, the major rejected to pay the pied piper his agreed fee, so the piper used his magic pipe to lure the town's children away.
It comes to my mind that the heroes could be hired not to find the flute, but to free - and hire - the piper, who is held somewhere in the dungeon. After that, the emperor could refuse to pay (this could just be told to the heroes by Mentor), the piper lures the children away and hides them in a dungeon, so the heroes would now be sent to find and rescue them (and perhaps pay the piper).
But at the other hand, it would me more fun if the heroes could play the flute themselves, having a horde of skaven following them.
Or you can make a Quest pack -
Quest 1. - The heroes fight against the Skaven, finding them too many to defeat.
Quest 2. - Mentor has found legends about a magic pipe that can enchant rats and related beings, so the heroes venture to find it. Of course, they try to use it at once, and make some comical effects (skaven following them a little distance), but must find out they lack the musical talent to use it properly.
Quest 3. - Mentor tells them, that the flute can only be played by it's rightful owner, the pied piper, who is for good reason held captive far away by the scaven. The heroes go and rescue him.
Quest 4. - Now they escort him to the scaven stronghold, so he can work his magic (besides lots of skaven, there should be also some of their allies, e. g. orcs, which the heroes have to fight off).
Quest 5. - Everything seems well, when Mentor tells the heroes that something has gone wrong: the emperor, enraged by the exaggregated price the piper asked, had refused to pay him. Now the piper has lured the capital's children away into a deep dungeon. The heroes must find him, free the children, and either pay him off or kill him. He could have charmed some skaven to serve as his guards.