What do you mean by you sabotaged their military?
While my rep with the factions are in good standing, I raid colonies containing military bases from a specific faction I want to silence. The attack starts with port disruption, followed by disrupting farms or heavy industries to effectively cripple their stability modifiers. I keep their stability to 0 as long as possible through disruptions or raids, do missions for that faction to ensure they don't have a good enough reason to enter hostilities, and sustain until the colony decivilizes and render the base inoperable. This an operation that normally takes more than 1 cycle alone, but shorter when I perform in conjunction with pirate raids in a system. I don't bombard since that is not covert, and knowing when and where to approach in between patrol gaps with the transponder off is rough without pirates distracting them.
The Hegemony and the Persean League has a lot of military bases, so I just plan accordingly by effectively decivilizing their heavy industries while pillaging their blueprints.
Spoiler
With the Hegemony's military colonies gone, they cannot deploy AI-Inspection fleets to colonies where I liberally use AIs.