Yaru can be nice, it just depends on usage. For example, you say you あげる something to a person, but you やる something to a kid or a pet. In this meaning of giving or supplying, or doing for someones favor, it talks down to the person you're using it for, so a person of similar status and especially superior status will not be happy if you use やる towards them.

In the meaning of kill, it's quite obvious in what ways it isn't nice, it's used when you're talking about killing someone. Watch any drama, anime or whatever with yakuza and this is bound to come up. It will not come up when someone is talking about putting down their pet dog.

Using yaru to talk about sex is obviously some form of slang.

Situations where yaru isn't a "bad" word could be something like やった！when you are happy that you did something. But yeah, it's a colloquialism, in the right situation, there's nothing wrong about using it. It is often used in negative situations though, so it's worth having been exposed to it a bit before using it.

First off, it depends on which use of やる you are talking about.  やる used to mean "do" (as a replacement for する) is not that bad in casual speech; it can even be used in informal speech with people higher than you.

やる used to mean "give", and やる after a -te form verb, are both highly context dependent, and they also depend a lot on gender, personality, where in Japan you are from, who you are talking to, and other things like that.  Probably in terms of your production, you can get away with never using やる in this sense.  This is especially true if you are female.

She did think it was funny when we were out to dinner and I said, ぼくはこの　おこのみやき　をやる。

That's when she said it sounded "dirty". I guess It might have sounded like I was going to have sex with the okonomiyaki (which I would have. It was delicious).