While this assessment does come from a reasonable place, I do believe that it may in fact be an overestimation of the difficulty.
In 40k, some Chaos guys created the Daemonculaba, which were mutilated, mutated women and made to birth live Chaos Space Marines. Some of those born in this way were born mutated, disfigured and without skin, called the Unfleshed, and were flushed through the sewer systems to die. Some however survived, and not only did they survive, they weren't evil and worshipped the Emperor. Also all this was happening on a Daemon World.
So yeah. Chaos mutants born through Chaos sorcery on a daemon world, yet were Emperor-worshippers and good people. If we took a skaven baby and grew it right with Order gods in mind, that might all that be needed to take it away from Chaos.
EDIT: "For little gain" is probably correct though. Very few skaven actually have the potential to be heroes and such, while most are just slave stock and the like, and skaven have very short lifespans no matter what. Just not worth it.
EDIT2: Shallya would love us for it though.