This seems to me a bit poorly thought out event, given the current unbalanced manpower. Seps/HF are not just the underdogs, they're practically non-existent! Props for the team for setting it up anyways.
I feel this would have been better if the Seps / HF actually got some targets to attack (for example place a Battleship at Norfolk, a fuel depot and the cruisers in Texas, and maybe an ammunition depot or whatever in Bering). That way you split up the overwhelming Navy force and give Separatists a chance to "win" if they manage to sneakily take out, let's say, 2 out of 3 targets. The Navy would have to run patrols around the targets and prevent any Separatist counterattack to win. This kind of idea is proven to work in other (team based) games with shorter game sessions, where it's called Objective / Insurgency mode (although sometimes the objectives are hidden at first and the attacking team needs to collect enough intelligence to reveal them).
Unfortunately I have given up on the idea of "persistent" war that Binski is campaigning (against the windmills) for actually working with this game / community / universe. There just aren't enough player numbers / player slots / servers in different timezones for such a vast galaxy as Freelancer's. Way too many sides / factions / conflicts going on at the same time, and the already mentioned 3 am logging for lone sieges problem (although I feel that one would be partially fixable with a smart balancing plugin that would just make bases invulnerable if there aren't enough IDs of a participating faction logged on for both sides)
But I do believe it's possible to run bi-weekly / monthly events with a similar theme and a time-limit (to minimize the chance of low pop abuse), just for variety, so it's not always about pewing / collecting blue messages.
(I may sometimes sound a bit like a Binski alt account, but I can assure you I am not! ).