I think its a bit weird that the player eats soap with this mod installed. Do you think it would be possible to change the animation and sounds used for it so it does not look like you are eating soap?

Yup, thaumcraft sanitizing soap has using animation

Agreed. This is something I wanted to do but haven't looked into how to do custom item usage animations at all yet.

Well, Thaumcraft 4 did it with their soap.