And think of this.......
It would take about 2 initiative passes to activate 3 agents and take no other actions. And all of the requested actions would be complety out of sink.....
Firstly, your comment on running a program is only applicable when a deck is booted or a program needs to change (say, when swapping Baby Monitor for Encryption, or loading an Agent into an empty program slot).
Secondly, if the Control Device action (p238) can be used to control multiple devices as long as the command is the same to all devices, surely Send Message can perform the same function.
Example:
Decker X (single Action Phase):
Simple Action: Send Message "Agent 6, sleaze a MARK on the owner of [AR marked maglock] and then spoof a command to unlock it"
Simple Action: Send Message "Agents 1 through 4, assist Agent 6 in it's task."
Since an agent has both the Hacking and Computer skills, the Matrix Perception, Hack on the Fly, and Spoof Command actions would be intuitive to it, and in my opinion would not require a Pilot/Agent test to see if it understood the order (p269). The Agents would proceed somewhat as follows, assuming average initiative rolls (12+14 for the Rating 6 agent, 6+14 for the Rating 3 Agents):
Initiative Pass 1: Complex Action - Matrix Perception (Who is the registered owner of maglock Icon?")
Initiative Pass 2: Complex Action - Hack on the Fly (Owner of maglock Icon)
Initiative Pass 3: Complex Action - Spoof Command (Unlock maglock)
Thirdly, to my mind there are ways of making the kind of of thing the OP has suggested work in the current SR5 ruleset. Just because those ways are aren't necessarily explicitly spelled out I see no reason to restrict a player from coming up with a great idea and using it in an interesting fashion, any more than I see a reason to restrict a street samurai or magician who thinks of using his or her environment to their advantage during a combat scene. Is it rules as written? No. But the rules as written contain these very important sections on page 44:
"The rules are here to help you move the story forward, to give you outcomes for the decisions you’re making. They are not a perfect mirror of reality—at times, the rules provide abstract ways to determine the results of concrete actions, because it speeds up the game and prevents players from having to roll dice over and over again to complete certain tasks."
"Role-playing is a cooperative endeavor, and every member of the gaming group should be working together to help each member of the group have fun (even the gamemasters, since they should occasionally be allowed some enjoyment). Players should feel like their characters can play an important role in shaping and advancing the story, and the gamemaster should feel that they can keep the story moving ahead without having to engage in prolonged and distracting discussions about the rules."
To summarize; to me the game is about having fun, and if the rules don't contain the necessary provisions to make something I want to happen, well, happen, then I either handwave it or come up with some rules on my own. Rules for scripting and mooks may not exist in 5th (yet), but there's plenty of rules in 4th to base a new framework on, and even without that it's simple enough to implement with very little deviation from the core SR5 rules.
In this case, the OP has come up with a unique way of creating a pocket hacker that has significant drawbacks, costs a decent chunk of money, but that gives a team with no dedicated decker matrix support of a kind. I think that should be rewarded.