1 is an extreme fringe case though right? Be honest, how often do you actually toggle the thing on and off in a play session and how many times has it impacted you to the point where you were inconvenienced enough to "need to do it after a jump instead of before"?
Anyway, relatively straightforward counter to it is "you can't engage your shields until you have the power for it either". Shields need power. You lose that power, the downside is you can't toggle shields on or off and it takes time to bring them back up even once power is back online. You're wanted. This is a downside to that. I don't think this fringe case event warrants any particular attention here. By the way, the delay is around 15 seconds. If you engage it the moment you drop into a system, there's no way this is going to impact you.
2 - bugs need to be addressed and fixed. Other things need not change to accommodate the bug, the bug should just be fixed. That's that.
What's happened here is someone wanted to do it when their ship was wanted, then found out why they couldn't and chose to remain angry at the game for it, rather than just go "oh ok, won't do that again then" and move on. It's not controversial. I don't think we need to keep talking about it. Your position began and concluded on the sole basis that you think it makes no difference either way, a position I disagree with, and yet then you appear to now think it does make a difference in two ways.
My only feedback for this feature is it doesn't appear to be covered explicitly in the pilot's handbook (at least not the one in game). This could change but I doubt the OP would have gone there anyway.