I think you really need to read more about the phenomenons. A good place to start is the FBI Freedom of Information Act server, which contains several full packs of info on cattle mutilations. The Institute of Discovery Science is also a good place to go. Clearly though, you haven't really given thought to the subject because there are plenty of logical reasons one would give.
-Cow modulations
-Constant sexual activity with abductes
-Medical procedures which are useless or even inferior to our medical technology.
-Explaining advanced and mind altering concepts to people that won’t be able to being that information constructively to the rest of the human race.
-Making sure the masses of humans can’t be assured or even recognizes their existence.
In biological research, we do some of these things, (accept have sex with animals), and some of the things you are saying are not things I have read abductees claim - or at least, they aren't mentioned by UFOlogists I've read. Then again, I tend to be more careful which sources I read than most. Perhaps you are assuming that all UFO litterature has the same level of authenticity? It is hardly the mark of a true skeptic to not look into each individual source of information on a case by case basis. Anything else is biased thinking.
Working under the assumption that cattle mutilations are real, one needs only look at the actions of biologists to get a clue what they are doing. We ourselves mutilate animals in biological research all the time. We dissect animals, we harvest there organs, and we run experiments with there tissue. Then, we discard the body. The only part of this idea that doesn't make sense is the mannor in which the cattle are disposed. Why return the cattle to it's field or origin? There are countless other methods of disposing of the corpse which would leave no evidence at all. I fully admit that I have no answer for this question. That however, does not disprove anything; it only means the case is not solid.
With reguards to medical procedures, I would have to ask for you to specifically state what you are talking about. Every Tom, Dick, and Harry who has supposedly been abduced have described everything from being forced to have sex with alien females to sperm removal, to dissection. Abducted women describe induced pregnancies which later dissappear to likewise having sex with alien men. In the cases of humans being forced to copulate with aliens, I'm sure you are familiar with the concept of beastiality. If we are going to apply human standards of behavior, why not? Some people get a kick out of, some are more turned on by that than anything, and I've even heard it mentioned by some members of that sub-culture that has been in some human cultures, a norm.
I'm out of time, but here are a few points to think on.