(Im new to scripting myself, but am a seasoned programmer and have been reading a lot, so this is just an idea, this aint actual code (but as far as i can work out this is one way of doing what you wanted))
create your checkpoints, with at least on troop in a squad there with a known name. set a trigger on west present at each check point, and in the "on activation" run a script:
[player, "sentry1"] exec "checkpoint.sqs"
checkpoint.sqs would need to do the following (see command reference for syntax)
_plyr = _this select 0
_guard = _this select 1
disable user input
create a camera pointed at the players vehicle, near the checkpoint.
set unit _guard to look at _plyr , _plyr to look at _guard
_guard say "Halt!"
~0.5
_plyr say "Here are my docs, let me past"
~random 2
? !discovered : goto approved
#attack
set combat status or side info etc
goto #end
#approved
_guard say "ok"
~0.5
_guard move
goto end
#end
cut back to original camera
enable userinput
This assumes that a varaible "detected" be set to true when enemy know of assasination.
What hapens?
get the player and sentry units names
if player has been discovered, then enemy will "recognise" you, and get ready to fire, at this point the player will regain control and can escape/attack, if not discovered, sentry moves asside, and player is allowed to continue driving.
Think that covers it. If you use de-pbo you can pull appart the built-in missions, they have several such conversations that you can base your own on.
Mister W.