- Smith does not need or want to kill Morpheus (in the matrix, or the real world); he needs to catch him.
- Smith is "so riled up" to catch Morpheus because he sees this as his only way out of the matrix.
- Smith would kill Neo or Trinity to accomplish this, but almost certainly not at the expense of letting Morpheus escape.
- It is not absolutely clear that the point of the strike would be to kill the humans (at least not Morpheus); it could also be a "plan B" to try and keep Morpheus plugged in.
Like many a good Matrix-universe question, I wasn't sure if there's a direct, succinct, satisfying, explicit canonical answer (disclaimer: the games are a blind spot for me, and I think there are a few comics I haven't seen).
I started with the exchange you quote and worked my way out (without knowing for sure where it would lead), so I'll preserve that process below the rule to show my math.
The script (numbered shooting script, March 29, 1998 -- may differ slightly from actual dialog) has a smidge more context, here:
169 EXT. ROOFTOP - DAY
We rush at the roof access door as it suddenly
slams open and the three Agents charge out. But Neo, Trinity and
Morpheus are already gone.
The trace was completed.
We have their position.
Order the strike.
Agent Smith can't stand
listening to them. He moves to the edge of the building, looking out
at the surrounding city.
They're not out yet.
They aren't all unique to this scene, but it suggests a few things:
- Machines outside the Matrix keep the agents in the loop, presumably via their earpieces.
- At least in this case, one or more agent has command-control authority over the sentinels. I don't recall if it's clear from the actual scene--either they all have this authority and Jones actually initiates the strike, or Jones is telling Smith, suggesting Smith alone has this authority.
- Whatever agents are (the consciousness of a machine connected to the matrix? programs? [I'm not sure if there's a "difference" between these...]), we can't safely reason about them as a homogenous group.
- At minimum, Smith's thinking (and maybe motives) at this point differ from the other agents. They may be diverging, or Smith may be fundamentally different.
Moving beyond this scene, I think we can infer a little bit more. I'll focus on the strike, first:
- After thinking through it, the machine/agent objective of the sentinel strike is uncertain. The obvious purpose is just seek-and-destroy, but it could also be a last-ditch attempt at keeping Morpheus in the matrix where they can continue trying to break him. Both cases are predicated on reaching ship before everyone is out of the Matrix (or the humans would just use the EMP).
- The Nebuchadnezzar doesn't detect the sentinels and sound an alarm until scene 181, immediately after Neo kills Smith in the subway station and Smith hops off the train in a new host. In scene 182, Morpheus says they have 5-6 minutes, and the sentinels finally land on the ship in scenes 199/200, while Neo is running up the fire escape.
- If Jones initiated the strike in scene 169, it took a long time (the entire duration of the subway scene) for the sentinels to get close enough for the hovercraft to detect them plus additional time to reach the ship.
- If the strike is predicated on reaching the ship before everyone is unplugged, it seems like the sentinels would hold for the order as close to the ship as they can get without being detected.
This seems like reasonable support for seeing the strike as Smith's call, and for assuming that Smith doesn't call the strike until Neo kills him. Let's dig into what Smith might be up to, here.
- Smith says "They're not out yet" after Jones suggests ordering the strike, but the fact that they aren't out yet probably isn't the reason not to order the strike; the strike would be pointless if they were. I don't think Smith is directly responding to the suggestion.
- After Jones (presumably) suggested ordering the strike, the script also says "Agent Smith can't stand listening to them". Brown and Jones aren't chattering incessantly, so this reaction is probably about what they're saying and what it means. If the strike is a risky "plan B", proposing it indicates Brown and Jones have rationally concluded it is more likely to succeed than "plan A".
Next, let's turn to the elephant in the room--the subway scene. The next 2 scenes after Smith's statement are worth reading in their entirety:
170 INT. SUBWAY STATION - DAY
An old man sits hunched in the far corner of the station, shadows gathered around him like blankets.
Mumbling, he nurses from a bottle of Thunderbird when -- A PHONE begins to RING.
Neo leads Trinity and Morpheus bounding over a set of turnstiles towards the ringing phone inside a graffiti- covered booth.
Let's go! You first, Morpheus.
Morpheus gets in and answers the phone.
Lost in the shadow, the old man watches as Morpheus disappears, the phone dropping, dangling by its cord. His eyes grow wide, glowing white in the dark.
171 EXT. ROOFTOP - DAY
Agent Smith stares, his face twisted with hate. He will never be free of the Matrix.
He starts to turn from the edge of the building when he suddenly hears it, his head whipping back around, staring--
Heh! We actually get a fairly unambiguous clue. Smith's goal up to this point is getting the code from Morpheus, and his motive is freeing himself from the matrix. This suggests:
- Smith does not actually need or want to kill Morpheus (in the matrix, or the real world); he needs to catch him.
- Smith would kill Neo or Trinity to accomplish this, but probably not at the expense of missing a chance to re-catch Morpheus.
- Smith is probably unwilling to order the strike because he's overconfident or in denial about his ability to keep Morpheus from getting out, relative to the risk of losing Morpheus in the strike.
As soon as Morpheus escapes, I think Smith's goal and motive both become vengeance.
Note: The Morpheus interrogation scene is also good reading here--it touches on many of these issues--but I managed to answer the question at hand without working out that far.