Like many others, I left TF because I wasn't comfortable disabling SIP (Yes, yes, I know. Our systems ran just fine before SIP, but still...). Anyway, I just came across this post and the update by @rjrggr and decided to give TF another chance. I can confirm that @rjrggr's tip works as advertised with one minor change.
After moving TotalFinder.osax to /System/Library/ScriptingAdditions and re-enabling SIP, TF continued to work fine except for changing certain options. In particular, options that require a Finder restart such as disabling tabs. Presumably because TF needs to write to /Library/ScriptingAdditions/TotalFinder.osax and it isn't there. I suspect that TF updates would also fail for the same reason.
The problem appears to be solved by a simple symlink from /System/Library/ScriptingAdditions/TotalFinder.osax back to /Library/ScriptingAdditions (I did this In a regular login shell; no need to boot to the recovery partition). All options now seem to work, I have column autoresizing goodness and fully enabled SIP. Yay.
p.s. @darwin's tip works for me as well.