There really aren't better ways to solve that on a mass scale at this time. I intend no offense but to be honest I care much more about my system's security vs your need to interpose system processes. SIP is a step in the correct direction for security. Is it perfect or a catch all? No of course not but it's another layer of security that helps the situation overall.
I recommend that you tally up the revolutionary technologies produced over the last 30 years that allowed us to get to this point (including the web), and then consider how many of them could be invented on Mac OS or iOS today.
