Can't you simply change the missile model and fx to instead appear like a Federation shuttlecraft or runabout and then explain it as the Federation using troops to clear enemy occupations from the planet's surface (phasers set to stun, of course)? Alternatively, Sins has a mechanic whereas capital ships slow the spread of enemy culture at a planet they're at, so maybe it would be possible code-wise to enable Federation culture spread to be bolstered by having Federation capital ships at
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