On the other hand, no one needs to know who it was? I mean we are going in disguised so well that both magical detection and fate itself have no clue who it actually is? So if we kill everyone in a way that no one would attribute to the Mage Killer, then no one will realise it was Kiritsugu? They will know someone wiped out the Einzbern, but any attempt to find out who it was will fail miserably. No one knows we are an exalt, and so no one would attribute this to Kiritsugu?
Heck, we could even frame someone else if we wanted to? Take the appearance of someone like say Zouken Matou and "accidentally" allow ourself to be seen in the surrounding towns just before the massacre.
We can disguise Ilya without too much trouble. I think theres a Cecelyne charm that allows you to grant mutations via wishes, and one such mutation is cosmetic changes. Change the color of hair and eyes and no one will make the connection. Heck, Malfeas also allows that if we get by rage recast.
Its possible to wipe them all out, get everything valuable, and then go into hiding until the heat dies down.