I agree with this one for most of its applications. For some things such as prop pushing/mic spam (if unintentional) I think there should first be a verbal warning (literally just telling them the rule) so that they don't have a record right off the bat for a genuine mistake.
Adding onto this, I think we should definitely revert to the previous system until a better option comes to mind (possibly on other responses to this thread). I have experienced the bad part of this as an RDM fest made it look like two people were Ts resulting in me killing them both and finding out they were innocent. Since I had used an MP7 I ended up going from 100 karma to 72 karma because of a misunderstanding. It took me way too long to get back to 100 karma because the karma you gain was also decreased. I think if the per-line-reduction system is going to stay, at least bump karma gained per kill back to what it was before the update.
I feel as if giving the missiles health would be a lot of work and might just make them too weak. It'd kind of be like a hurt station but everyone would see it and shoot it down instantly. I feel as if a better alternative would be to flat out remove the following missile because it's kinda overpowered (you can literally throw it straight up in the air and still get kills) and, as you said, set a timer or distance cap for the controlling missile. I don't know if the regular missile should be changed though, honestly. It's pretty basic and hard to use right anyway since it's so slow and easy to dodge.
Overall, this is a very well thought out post and props to you for making it. 👍