As Matt said, there are going to be places where Thorton is forced to fight. Now, stealth and patience can certainly allow some players to bypass the thicker encounters with some cunning, but a hands-off run is not a plausible strategy.
There are certain missions in Alpha Protocol that involve getting in and out without touching people or alerting anyone. In certain situations, this also provides opportunities to score points with contacts and handlers.
However, not all missions are like this. There will be situations where Thorton will be forced to fight... just not forced to kill.