#1: The problem here is that Butcher set up the world with a Creator. With the first law your trying to break his basic rule, "Thou shalt not kill" without consequences. I don't think you can. I'd argue that even when the Wardens kill with a sword it stains their soul, just not in the same way as with magic. The White Council can stop people from killing with magic but not killing without it so they only care about the former, that doesn't mean the latter is any better. Talk to you local religious figure about how you can kill someone and yet not be responsible.
#2: A properly researched, well thought out ritual to transform a person which takes into account all the consequences for storing their soul/mind/personality and allowing them to transform back at their will probably doesn't stain the soul. Spend a few decades doing the research on that one.
#3: The problem here is "invade". There has been a lot of discussion that if the invasion is voluntary then it might be ok, or if its just looking around. Yea sure, some of those particularly the looking into a voluntary subject might not stain the soul. But its too tempting to do a little tweak while in there, or look at secrets the person has. While in someones head can you resist the temptation to see what they really think of you? Probably not and if you do you just crossed the invasion line. The Council has determined that even defensive mind magic seems to be too close to breaking this law so they don't even teach anything beyond the basics. That seems a bit too far but its so the temptation never exists. To break this one I'd say it has to be 100% voluntary, no coercion, no threats, not even a you need to prove you innocent type of thing, and then only looking and only looking at the specific info they allow. Well if you meet all whose conditions there really isn't a reason to look is there?
#4: Any enthrallment is a stain, this one is clear. You can't make someone do anything, even love potions without negative effects.
#5: The stain only seems to apply to crossing the borders for things with souls. Sue was an abomination, but not a killable offense. Raising an army of zombie bunnies seems to at least tolerated. Again this comes back to the Creator issue. He won't like you bringing back the dead, what Koumari does will noble probably violated the Creator/Universes rules about that.
#6 I don't think the 6th stains the soul at all, its just such a bad idea to go back in time that it has to be stopped. To many actions messing with the past lead to breaking the "thou shalt not kill rule", even if you don't use magic beyond the time travel part. Changing history means someone out there died who didn't before and you were the cause. You could probably go back, veiled, levitating and incorporeal leaving no trace and record events without causing a stain but extreme precautions would need to be taken not to influence anything. Precautions which are probably so difficult as to be impossible.
#7 The 7th has a lot of leeway. Research that never contacts an outsider probably doesn't hurt at all, its just that those who start to research write it down and other people pick up that work with bad consequences.
Dealing with one is just a road to corruption.