I'm not sure if I understand.
Each system has only one stargate, right (or most of them, at any rate - Sol probably has more than one)?
So, say System A is largely controlled by the Free Colonies (i.e. they control the gate), and they want to attack System B, which is SU. Their options are to
1) inaccurately send some pilots in a lifeboat to somewhere in the system and hope Free Colonies sympathisers on the other end can pick them up in time, or
2) accurately send them to the stargate. They'd probably have to send mecha with them, or maybe if the TTM were lax (which seems unlikely) a couple of pilots could be killed in their sleep and their frames hijacked.
Is that roughly how the gates work? Or does the presence of a gate on the other end make it possible to send stuff anywhere in the system with greater accuracy than with no gate?
And if the Ijad goal is simply to eliminate the Solar Union's ability to maintain an empire that threatens them, why can't they send nukes to every SU and Free Colonies stargate?