I don't know... since Skaven cannot have axes there is nothing that players could confuse the weapon with. You know what I mean? WYSIWYG does make sense when models with axes are meant to have swords but since the Pestilens rats cannot have axes at all there really is no potential for confusion.
I also wonder: are you converting the weapon for fun or to please your gaming group? In our group WYSIWYG is not a problem, so there is no need for these kinds of conversions. It is only relevant for official GW tournaments, but there Clan Pestilens is unlikely to be allowed anyways.
All in all, if I wanted to convert the model, I'd just give it a proper skaven hand with sword rather than try to amend the skythe to look like a sword.
EDIT: Oh, and moved to Painting and Modelling as this is not really a rules question.