Hmm... I'm not sure I agree with all of this. Let's see-
1. Restricting ships' control systems is never a good thing. It's an artificial, specific piece of balancing that isn't very sustainable either, particularly if we're going to get programmable systems at any point in the future.
Of course, the ease with which one can install internal guns is an issue, but a solution should aim to resolve that issue rather patch over it. Bringing the strength of an astronaut up to par with that of a small turrets, with things like personal armor, better shield-bypassing guns or maybe even personal radar jammers is one idea. Making it risky for some reason to have turrets firing freely in your own ship, which seems kind of sensible, is another. Outright removing the ability to aim for an astronaut is not.
2. This does make sense, no complaints here.
3. Can't really discuss this without personal experience.
4. This seems to boil down to the same issue as #1- ships can't hurt themselves, making it very easy to indiscriminately hurt boarders. For the time being, your proposes solution might be the easiest.
5. Again, artificially limiting ships' control systems isn't a good idea. The anti-boaring measure you're describing is just the ship refusing to actively assist boarders, which seems perfectly reasonable. Besides, it's not like this is making boarding impossible. Boarders are under no obligation to be in gravity in the first place (gravity modules can be ignored, are triggers can be torched) and could just space-walk their way up the lift.