Would it be possible to create a new classification of minor faction?
Just off the top of my head here, a "rebel" faction could have certain criteria to meet and essentially go through the same process as going major; except that they're intentionally staying minor with the intent of rebelling.
That way, folks like the Vagrant Fleet or the original Rebel Alliance (who wanted to stay minor, if my memory is correct) get the nod as being established enough to engage in rebellions where as new minor factions X, Y, and Z have to wait a month and get five unique writers.
Faction aide? I'd say during Rebellions, give both sides half as many ally slots as invasions. The offense is minor faction, so rationalize it as limited resources or something. The defense is being caught off guard by a rebellion, so they wouldn't have its full might.
And then, since the proposed ideas would essentially allow a Rebellion to strike anywhere, add a detail about what happens if they fail. If the major faction defeats the minor, the Rebellion will be considered "crushed" and said minor is demoted to the same standing as all minor factions for x span of time. (Loss of resources during the fight and all, recovery. Etc.)
I don't know what can be done about alts, save for saying point blank that alt-padding a rebel faction isn't tolerated and if it seems like that's happening then there will be consequences. Traditional abuse and suffer mantra.