"it only says she can negate any skill she wants including The End"
Yes, that's exactly the point. It is literally said by herself she can negate ANY power, which is what this power is about.
Also, you do know that for Ajimu to negate Medaka's The End, that means she also negates her Power Anchroing in order to do so, right? or else she wouldn't be able to negate The End.