The whole premise of this thread would be that there's a reason for the "rank system" to exist in the first place- specifically in regard to the "big 3 factions".
As it stands currently- there isn't... so it's really a pointless speculation. FD will need to make it meaningful in some way (exclusion or not) in order to facilitate a reason to do make Alliance vessels exclusive- as they've already started to introduce them without exclusion. Hell, excluding other rank-locked ships behind an arbitrary "faction wall" currently is already pointless in and of itself.
The problem isn't the ships. The problem isn't really the Faction system, either. It's that there's no definitive game play reasons for the Factions to really even exist except for lore purposes.
You go Federation, there's still no restriction to buying Imperial ships, docking at Imperial Stations, taking on missions, and vice versa. If it were implemented as a restricted system of some sort there would be incentive to "choose a side", and with the lack of such incentives there's really no point in doing so with the Alliance, either. Only difference right now is that the Alliance doesn't have a mission-system unlock path for rank-walling ships. (yet)