My experience is that it already is easier to stab someone when their are less militia and allied troops. Your own realms troops may or may not help you in your mission, I'm not quite decided yet. Having troops that are allied with you own realm in the region, appear to actually make it harder to complete a mission, which can be annoying. From my last 5 stabbing attempts, I think only 1 guy instant healed.
My hunches is that it does matter, regardless of realm of affiliation (probably for coding and balance issues I guess).
Infiltrators could also become to demolition tools what traders are to caravans...
