What are the consequences of the two options aside from fixing the original issue with git rebase? Should I be worried about some critical OS feature being disabled with option A or very slow git performance with option B?
This leaves you with the option to disable the core.trustctime setting, which I believe has no noticeable performance drawback for most or maybe all Git users.
If you are sensitive about the performance, perhaps a third option would be to make an alias for affected commands, especially for rebase:
_rebase = "-c core.trustctime=false rebase"
Personally, I've never encountered this issue and I rebase frequently.