Maybe I'm not the only one with this issue, that's why I'm documenting this…
TS2 v2.4.9 stopped working some time ago (maybe with the 10.12.3 update, not sure) on my Mac at work. Finally I took the time to look into it.
I downloaded the v2.5.4 prerelease that doesn't need SIP disabled (or enabled but without debug as older versions). So I did disable SIP completely for the installation, as prompted by the new TS2 upon launch (even though I did have debug disabled already, so it was supposed to have worked).
When launching TS2 after this it asked for an admin password twice and installed
/Library/ScriptingAdditions/TotalSpaces.osax, but it didn't work still. (It's easily noticeable if it doesn't work, because I only use TS2 to disable animations when switching Spaces. But TS2 is visible in the menu bar and everything)
As nobody else seemed to have this problem in this forum I looked around and found https://totalfinder.binaryage.com/system-osax
I figured it might be worth a try moving
/System/Library/ScriptingAdditions/TotalSpaces.osax, which I did (launched Recovery OS and unlocked FileVaulted drive for this).
On a hunch I additionally gave everyone read and execute rights on
TotalSpaces.osax, since they had no rights at all and belong to
root:wheel, and my normal User is not even an Administrator…
After reboot TS2 works again once more! Unfortunately I don't know if moving the
TotalSpaces.osax or giving everyone read/execute rights did the trick.
Maybe the developers have some clues, or maybe this helps someone else.