An idea I’ve had in my head would be a secret hijacked vessel disguised among a fleet of other friendly vessels that would be more of a puzzle to deduce which the right vessel is and to then destroy it. You’d have to figure it out based on which direction it was moving, anomalous characteristics, ship traits, or communications traffic, etc.
Essentially, making it more of a puzzle and roleplay experience rather than showing up in a sector and blowing up the bad guys.
Something else that might be interesting would be using more of those courier style vessels that move about quickly. If they reach a sector border more than 4-5k away from a friendly ship (outside of jamming range), then an enemy fleet could warp in to reinforce the existing conflict.