This would be a system where you would have to take some time to figure out whats works best for each gamemode. And it also schould only trigger if players leave early in the match and it should not directly affect the objective.
For example lets take eggwars, on first thought you could do it so that if a player leaves very early, all generators on your home island get upgraded one level. While this would put you in disadvantage playerwise, you could fully equip your team faster and potentially reach middle before the other teams.
In SG i would just give Resistance II when you spawn without a teammate or he leaves before the grace period ends. This will reduce incoming damage by 40%, giving you a greater chance of winning against teams of 2.
These are of course only quick ideas that are not really thought trough and might not be good enough. Its also important that you never get a siginficant advantage over other teams by having less players in a team, the goal is to reduce the disadvantage.