So you're not OK with giving a site a fairly narrow range of sandboxed permissions, but you are OK with installing an opaque binary that can read, modify, transmit, and destroy nearly every piece of your data on your computer.
You have heard of open source software that doesn't need a browser to run, haven't you?
If you're not watching every step, every time, you're gambling the same way you're gambling with malicious code in a browser (though I'll admit it's lower frequency). Your privacy/security is in the hands of whoever is part of the chain you trust, and their security practices, completely aside from new exploits that could affect you directly. Open Source, binary, it's all the same in the end unless you're perfect in your observational skills. Sandboxing limits that trust. I'll even grant that it's technically possible to do the same thing with processes in Unix, which you could be doing - but it's hard, error-prone, and essentially nobody does it except the stragglers who haven't switched to virtualization (which is essentially sandboxing).
You're being paranoid. With perfectly justifiable reasons - everything you listed is possible, plausible, and related things have actually happened. But you're not applying the paranoia evenly.