Can I change the offset to 2s instead of 1024s?
No this is not changeable and in fact make absolutely no sense.
If it can happen that your time is off by 2 seconds suddenly then you should check whats the reason for this behaviour and try to fix it.
Shutdown NTP is not the best solution, because your system is left without any synchronization and how will you compensate this 2 seconds without a time step.
Normally there should be no time steps when NTP is running, only one step during startup if NTP detects that the client is off by more than 128ms. If there are additional steps during operating then there is something wrong on this system and you should try to find out what it is.