The reason no civilian casualties were of concern in the canon "A Canterlot Wedding" was because Shining Armor and Cadance's love blast healed any injuries on the sideThe shrinking spell Twilight uses to stop the Changelings doesn't have that same luxury, leaving in the air the general distress of being injured and seeing other ponies left injured for Jewelius to take advantage of.
Jewelius has insecurities regarding his masculinityHe has for years been secretly bitter over the fact that his aunt and cousin have been treated with more praise and recognition than him. While cunning, he's not brave or particularly powerful physically or magically. After he becomes king, he makes Prince Blueblood his servant and hires convicted stallions to replace the guards (both stallions and mares) he orders to be wiped out, but his closest minions — Vivian, Commander Hildread and Lieutenant Shackle — are powerful mares, and he desires to gain powerful offspring to continue his legacy from his marriage with Twilight Sparkle. He may not be willing to have other stallions in high positions because he wants to maintain the illusion of being the top male.