If you put it this way, pirates and non-military non-house factions shouldn't have capital ships either.
However, The Discovery Mod tried to balance all the factions, by introducing equivalent hardware to everyone (more or less and except for the damned nomads, wilds and phantoms, that have uber stuff)...
Trust me, there's no other way. Either take them all out, or keep them all in.
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Mephistoles