When a fight happens, people die. Sometimes it's the players, sometimes it's the NPC's. Either way, you suck it up and you roll with it.
On other news, I recommend you use large squads of mooks to slow down your PC's as they hack their way towards your big NPC's. However, be aware of your characters capabilities!
Be aware of the three H's:
1: Hacking
2: Hopping
3: Hardness
Be aware of each PC's Hacking capabilities, their primary strengths at dealing damage, their Hopping capabilities, the extent of their mobility through skills and spells, and their Hardness, their ability to avoid and soak up damage.
By keeping these in mind (and perhaps writing them down on a little notecard to make sure they stay there) you'll be able to make better, more party-aware encounters.