I tried the approach you proposed about a week ago. While I thought it would work, it didn't. Tried it extensively with several of our PBM savegames. Even someone with the Exheir trait would end up becoming faction heir after the current leader dies and the true heir (even if you removed all his heir traits, gave him exheir and someone else factionheir) takes the reigns.

The only currently proved to be working method is giving someone the Factionheir trait and killing the current actual heir, making the one with the trait the new heir.