Overall I'd say the Laws of Magic in the Dresden-verse are a little over-the-top in a "it's a bit artificial" kind of way.
That said, I think as far as the game is concerned they are meant to be there more to balance the game than anything else. Altering and reading minds is insanely powerful, heck even Mind Tricks in Star Wars games are pretty darn awesome and the D-verse allows much larger effects. I don't think anyone can argue that messing with undead isn't also very potent. Same goes with time travel. The Outer Gates bit is, I think, largely meant to be on a plot level (though personally I feel that the "researching" bit should just be a legal measure and not a game mechanic, depends on how heavy the GM wants the plot device). So Lawbreaker for all that makes sense from a purely game balance and plot perspective.
That leaves transforming and killing. Now, some transforming seems a bit silly to count as a lawbreaker, to me. If you are repairing tissue damage, removing scares, or a little cosmetic surgery, then that seems rather silly to slap lawbreaker on it (certainly over the top from a game balance perspective). If you are doing something that alters/destroys the mind, then that goes largely into the area of the first law. (Augmentation beyond a normal human could be considered similarly, or just on a game balance level as OP if you don't restrict it in some way). That brings us to the first law, which is a bit murky. Killing someone with magic. Now, from a purely RP perspective, killing someone with magic and normally seems about the same to me. If you purposefully incinerate someone with magic, you have to BELIEVE magic can be used to kill and that they should die. If you knowingly shoot to kill someone, then that's really no different, honestly. Seems a bit odd for the game to make a difference though. On the other hand, magic can be crazy-powerful, hitting huge areas and killing people from far, far away that couldn't otherwise be killed. Lawbreaker helps keep it under control if humans or sufficiently human-like creatures are around.
Of course, to go to the OP's original concern, I think there is something more interesting afoot from a different perspective. Presumably, if a non-mortal kills someone with magic, they don't change because they don't have any choice in the matter; it is merely part of their nature. On the other hand, I find it more odd the other way around. Harry can kill talking things with magic, things that can think and learn (yet can't change their nature somehow), and that's OK. Seems a bit screwed up to me if killing people is problematic. Something is really off with those ethics.
In the end, I think you have to take the power of magic and the universe and just consider magic to have very special rules. Magic alters you more easily and changes you more easily. These changes are overreactions to what you are doing compared to how it would work if you did it any other way. That's why you can't be a wizard-psychiatrist or bring a recently dead loved one back to life whereas if you could do it with science it would be OK (you don't see behavioral therapists or doctors turning into monsters)*.
*Worst case you get surgeons who are egotistical jerks, really, well, beyond the people who are monsters for other reasons.