How do I stop Skype from sending and downloading files as this is becoming company policy to stop viruses?

Skype will only do this if authorised by you.
Even then the normal downloads are upgardes unless they are files sent by another party.
If your company has a comprehensive anti-virus system and competent IT department then this isn't an issue at all.

I don't need to stop Skype updates etc, but files sent by another party.

So don't accept them, as they do not download automatically, but need user intervention.

There is no setting to turn of file transfers!