You'd have to switch the "seconds since epoch" count to TAI, and that would cause new formatting bugs because all kinds of software assumes that the minute changes on a multiple of 60 seconds since the epoch.
I think if there were such a thing as a different kind of epoch time that literally actually is "seconds since epoch" it would help a lot and work like you suggest.
It sounds like in your scenario, you would prefer Unix time to instead include the leap second, so that no rollback or time smearing behavior would need to occur. I believe the reason it does not has to do with simplicity: current systems rely on a day being 86,400 seconds, making each year (regardless of leap days) a multiple of 86,400. Leap seconds break this simple assumption. While it would be simple for a new time formatting system to take leap seconds into account, it is not so simple to go and retrofit all of the existing systems for a new formatting standard, and convince so many different groups of developers to change that much code while also agreeing with one another about the changes.