I also found this chase scene playing out differently than obviously intended by the author, and found the players "easily" keeping up with and shooting at Theodosia. As is often the case when such things happen, it's because you (the GM) have forgotten some rule or other
So, hindsight being 20/20, here are some pointers that should have made a difference.
1) Theo goes first.
No matter how fast the ninja-players are, nobody can react to something before it happens. The players may have been waiting for something to happen, clasping their weapons under their trench coats ready to lay down some Judgment, but the plan for the exchange was a discreet meeting, using the crowds as cover. This means no weapons drawn, as this would cause commotion, even panic, amongst the crowds. Only one player was to come forwards, the others staying back. When Orday gets smoked, only those succeeding in a sight based Hard (-20) Awareness test will be prepared for Theos surprise drop from above.
Theo goes first, and the best the players can hope for is to not be surprised, so they at least can get to act too. On subsequent rounds, Theo's initiative is D10+5, which should be higher than most players, at least at the ranks this adventure is intended.
The first round, Theo drops down, grabs the case, and then makes a Full Move and may choose to make a Hip Shot while doing so. When (if) the players get to draw their guns and shoot (or run), Theo will be 20 meters away, putting him out of charge distance of even the fastest acolytes (remember, he starts 10m away from the closest Acolytes, and moves 10m each round)
2) Dense Crowds.
Anybody not Hive Born must test Agility -20 if using Charge or Run (including Sprint). Anybody trying to shoot Theodosia take their BS at -20, as he uses the hivers as cover. Any misses (including bullets from Full Auto Bursts that do not connect) will most likely kill innocent bystanders. Be generous with Insanity points in this case, and play up the nightmares later. And don't forget the corruption points as stated in the book.
3) Walls & Stalls.
Theodosia may run up walls as if nothing, but the Acolytes can't. On the end of the first round, Theodosia has actually made it over the first wall, dropping out of sight. (see the map) Any players giving chase will have to run around, or Climb over (Full Action, Difficult Agility test)
Theodosia has more (2 Full Actions each round). While the players will have to choose between FullMove/Run to keep up or attacking, Theodosia can do both. If a character actually manages to catch up to him with a Run(Sprint), all they've done is place themselves in Theo's Point Blank range, allowing him a nice +50 Full Auto at effective BS 91 before he makes his full 10m move away.
Should a PC catch up to him with a Charge, remember Theo dodges at +10 (62), then makes an Acrobatics test at 52 to Disengage as a Half Action, followed by a Full Move, letting him end up 15m away, and still allowing a Half Action for attacks. Also, remember that his Hip Shooting allows him to make a single shot while moving if you'd like to use his other actions for other things.
So what does it take to catch him, then?
Even if an agile sprinter with a move of 4 succeeded in his running test, he would have to stop at the stall-wall, or run around. A fast and cold gunman could whip out his autopistol, and fire a full auto burst at Theo at close range on the first round (if he was not surprised). The crowds cancel the FAB bonus, leaving it at BS +10 to hit. Theo is aware of the attacks, as he faces the players, and may dodge as normal, as well as getting of a hip-shot on round 1.
See the map. Unless the players move, Theo will be (and remain) out of Line of Sight after round 1. If they move, their shooting options are limited. If they wish to climb a stall, that makes their first firing opportunity on round 3 (1 round to run to the stall, 1 Full Action to scale it (requiring guns to be holstered), then draw/aim/shoot on round 3 (most likely after Theo's move on that round, which should allow him to move around a corner)
It's easy to forget all this in the heat of battle, and some pointers along these lines would have been helpful BEFORE running the encounter