"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 Meta Power Negation is about, so yeah, she is a valid user. It was also never said she couldn't negate Medaka's learned skills, you're making that up, she simply says she can negate ANY skill, including Medaka's (who has Power Anchoring) and that's it
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? if she couldn't negate Medaka's Power Anchoring, she wouldn't be able to negate The End in the first place.