Seconds for computers, convert for humans
Time in seconds should be how computers see it.
Time broken up into minutes/hours/days is done for the convenience of humans - who cannot deal with large numbers - who knows that 2592000 seconds is a (30 day) month ? The time convertion routines will deal with leap seconds.
Slight complications with some applications, eg bank interest is computed in days - be they 86400 or 86401 or 86402 seconds long. Programmers will get used to this and will cope, it will become part of the 'tradition'.
Fiddle the issue now and we will just end up being hated in generations to come when they have a big problem to deal with - and their computers will not deal with them since that is not the way things will be done.