Well that might be difficult, since the current system only allows upgrading
TO a unique unit as long as it is a replacer, while non-replacer uniques can only be build as new units.
You could create an exact copy of their predecessors for that Civ (a fake-unique Swordsman so to say with the very same stats, looks and descs as the original, that upgrades into a Samurai), but the drawback would be, that this fake-unique would also appear in the list of unique units when selecting this civ. Or wait... isn't there an option to hide specific traits?

If so, and if it could be used to hide a unique unit, then this would be the solution, I guess.
The other approach would be to replace a standard unit with the unique (Swordsman with Samurai with toned down combat strength), but I guess that's not what you want.
Alternative upgrade options would be awesome, but unless Firaxis implements this into the vanilla game, you will have to wait for modders to have access to the source code before you will see fancy stuff like this. whoward69 created something similar for Civ5 (including a conversion of upgrades to fit the new class) and it worked very good, but he modified the DLL to achieve this.