People who aren't loyal to me tend to enter my base rather frequently. I don't like them snooping around, though. Is there a disadvantage to killing everyone who enters my base? So far, I've been holding off on ending too many lives, but the few times that I was forced into action, nothing bad seemed to come of it.
The downside to murdering ALL the agents is that you've got to store their bodies. If their bodies aren't in the freezer, anyone who encounters them will take a hit to their stats. This makes them less productive and more likely to desert.
Engaging in combat means that your minions are more likely to get killed, and they're also not engaging in whatever activity they should be doing instead.
Body bags and the freezer room are also high-heat, which means that enemy agents who notice these items are going to cause trouble for you.
Remember that your goal is to put forward a "totally harmless not at all evil" vibe - making an "entry" area to your base that is full of innocuous but distracting items will ensure that agents don't become hostile, and that they leave the island thinking it's just another island resort (which happens to house a futuristic army barracks, cafeteria, and a bunch of high-security doors...).
Another point to remember is if the enemy agents leave your island with no suspicion (the rings around them haven't gone red) then the heat level for that faction will go down. Killing tourists can also raise the heat level with that .
If your heat is suitably low across all factions and you have an island full of stubborn agents then the easiest way to clear them out is a Freak or Two