Just brain storming...
One, not being able to use the heavy weapons might keep your PC's alive. Might keep your Borg alive long enough to be a challenge.
You can always arm him with frangible rounds (which might not do much). Gel Rounds would likely be better. Of course capsule rounds are fun too.
Either way if the players are working under the same rules then it will mostly be hand to hand. Add smoke and jamming and you should be able to to turn it in to one wild party.
Two, You can tune the ranged/melee specialization of your Borg to to challenge your players. Most fun is if the Borg is mostly a ranged specialist but has enough melee to give them a challenge. Then the next time they meet you can show them what the Borg can do with a favorable battle ground.
Three, You want him in the Mana box so that he will be awake if your players gas the plane. Works for me. If you want him in the box, then likely they would put him in hour or half an hour or so before landing to get past inspection. No reason not to when you can use simsense to play any game or watch any trid you want. Or maybe the Borg and another teammate are in the middle of a marathon game session. You can see if your players wonder who he is playing with (especially if that someone is about to finally win against the Borg and then gets gassed at the last second). Once the game is interrupted, you have a valid reason for your Borg to come looking for what is up. Might even have a fiber optic cable running to the box which neatly leaves the game off the jet's network and off the wireless (one again some thing for the players to question.)
Four, I'd also suggest more than one manabox. The extra one (which of course is closest to where the PC will come in is for the team mage).
Five, And there is no reason for a truly paranoid team to not ward the plane (or at least a section of it) once the wheels are up. Nothing too heavy. Just enough to shield the presence any illegal gear they might have and to alert the mage if anyone tries to enter. Makes the team feel better to be behind wards for mission planning too.
Six, in order to be sure you get to have the return of the Borg, the Borg has an internal parachute built in or has one strapped on. Maybe the players will blast him out the side of the plane to get ride of him. Might be a good tactic if the plane is filled with smoke. Worse comes to worse, he will make an exit and wait till he is out of sight before deploying the chute. Maybe the Borg will choose to grab a team mate and escape rather than risk capture (or even jumps after a team mate that gets sucked out of the plane).
If the Borg is unconscious, his internal systems will deploy it for him. Either way, you get to bring him back some time in the future which is always so much fun.
Seven, The bad part is if they gas the plane successfully, the borg will be all by himself. Maybe a spirit told to do what the Borg tells him to. Maybe a few drones to help out? They might be locked down for travel and or unloaded, but a rotor drone barreling down the center of the plane would provide a useful distraction even if the LMGs are unloaded. A ferret with a taser would be ready to go once unshipped. Either one could play chase the mage! So the Bork will want to crack open some drone travel crates if he can before engaging.
Eight, If they were flying a cargo plane, (perhaps they are bringing in a vehicle too) then you could have the fun of the rear ramp being lowered while the plane was in flight. Course you would have to take the risk that your players would also liberate the vehicle being transported and a cargo plane might be more expensive than a executive jet.
Nine, Course it is all ways fun to force the PCs to change plans at the last minute. What do you mean the flight has been canceled? They are suppose to take off in 2 hours. Wait got a private medium cargo plane, a Alenia C-27J, that just filed the same flight plan. Give me five to check on who hired it.
Lots of options to keep it from being a cake walk for your players.
You have to let us know how it turns out.
Man I have got to figure how to get my players in the same situation.