The biggest problem, in my opinion, is that as of now there's no way to play RBG and avoiding getting matched against those premades (edit: at least on Blackrock). Previously there was: disabling cross-faction and queueing from the same faction of those who are premading. Now if you queue RBG you're forced to (probably) enter that AV as Horde, where your team is getting camped, even if you are ally. Since players can and do react to this, this affects their participation and queue times.
As proposed, a middle ground could be to disable forced cross-faction only for those big BG maps, so that Alliance-faction alt characters can be forced to play Horde, just not for AV/IoC. Sounds easy to implement, doesn't affect anybody negatively and adds choices to players, with the effect of also increasing BG activity. Besides, it partially (only for AV/IoC) reverts to a previous situation, as stated above.
Yes, with this measure Horde will still enter the AV/IoC game and be camped, but at least they can login their Alliance chars (if available) and play RBG without being forced into playing against AV/IoC alliance premades.
No, that's not the reason. The reason is there are very determined (and skilled/coordinated) players which are currently playing in the Alliance faction. They were in the Horde previously and the situation was symmetrically opposite, so the causal relationship is easy to establish. What this post/suggestion does is merely considering the effects of this, and proposing ways to improve the situation.