There's a few things happening here.

According to the script, we first have the scene you refer to between Worf, Troi, and Riker occurring on the bridge:

WORF: Sir. Permission to speak frankly.

RIKER: Go ahead.

WORF: Our priority is to stop the aliens from any more incursions to Earth. Any delay is unacceptable.

RIKER: If I can save Captain Picard, I consider that very acceptable. WORF: The Captain would not. I recommend we target photon torpedoes on the alien habitat and destroy it. Immediately.

TROI: He's right, Will.

RIKER: Power up the photons, Mister Worf. Alert me when they're ready.

Presumably at the same time, you have this scene, which you also vaguely refer to, happening in engineering:

LAFORGE: Computer, initialise the reload circuits.

COMPUTER: Reload circuits are initialising.

LAFORGE: Okay. Data? This ought to do it. (does something to his positronic net)

LAFORGE: I don't get it. I don't understand why isn't this working. Computer, run me a diagnostic on the input polarisers.

COMPUTER: There is intermittent contact in the input polarisers.

LAFORGE: Intermittent? (Geordi opens the back of Data's head)

LAFORGE: What? An iron filing. How'd that get in there?

And then you have this exchange immediately afterwards back on the bridge:

WORF: Commander, I have set the photons to fire in staggered rounds, detonating in ten second intervals.

RIKER: Very well. Fire when ready.

WORF: The sequence will be ready to initiate in one minute.

This seems to show that Worf spent a small amount of time instructing the computer to use a particular firing solution while LaForge was troubleshooting some issues with restarting Data. As a result, the computer will need about a minute in order to calculate the firing solution and prepare the required number of photon torpedoes to execute the solution. This one minute of calculation then allows the next scene to occur:

LAFORGE: Computer, run another diagnostic on the input polarisers.

COMPUTER: Polariser circuits are functioning.

LAFORGE: Well, then, that ought to do it. Okay, Data. Come on, now.

DATA: Torpedoes. Phasing. Alien. I am processing a binary message entered into my static memory by Captain Picard. Geordi, are we planning to fire on the alien habitat?

LAFORGE: Yeah, but

DATA: It is imperative that we do not. I will explain later.

LAFORGE: La Forge to Riker. Hold your fire!

There's a few things happening here.

According to the script, we first have the scene you refer to between Worf, Troi, and Riker occurring on the bridge:

WORF: Sir. Permission to speak frankly.

RIKER: Go ahead.

WORF: Our priority is to stop the aliens from any more incursions to Earth. Any delay is unacceptable.

RIKER: If I can save Captain Picard, I consider that very acceptable.

WORF: The Captain would not. I recommend we target photon torpedoes on the alien habitat and destroy it. Immediately.

TROI: He's right, Will.

RIKER: Power up the photons, Mister Worf. Alert me when they're ready.

Presumably at the same time, you have this scene, which you also vaguely refer to, happening in engineering:

LAFORGE: Computer, initialise the reload circuits.

COMPUTER: Reload circuits are initialising.

LAFORGE: Okay. Data? This ought to do it. (does something to his positronic net)

LAFORGE: I don't get it. I don't understand why isn't this working. Computer, run me a diagnostic on the input polarisers.

COMPUTER: There is intermittent contact in the input polarisers.

LAFORGE: Intermittent? (Geordi opens the back of Data's head)

LAFORGE: What? An iron filing. How'd that get in there?

And then you have this exchange immediately afterwards back on the bridge:

WORF: Commander, I have set the photons to fire in staggered rounds, detonating in ten second intervals.

RIKER: Very well. Fire when ready.

WORF: The sequence will be ready to initiate in one minute.

This seems to show that Worf spent a small amount of time instructing the computer to use a particular firing solution while LaForge was troubleshooting some issues with restarting Data. As a result, the computer will need about a minute in order to calculate the firing solution and prepare the required number of photon torpedoes to execute the solution. This one minute of calculation then allows the next scene to occur:

LAFORGE: Computer, run another diagnostic on the input polarisers.

COMPUTER: Polariser circuits are functioning.

LAFORGE: Well, then, that ought to do it. Okay, Data. Come on, now.

DATA: Torpedoes. Phasing. Alien. I am processing a binary message entered into my static memory by Captain Picard. Geordi, are we planning to fire on the alien habitat?

LAFORGE: Yeah, but

DATA: It is imperative that we do not. I will explain later.

LAFORGE: La Forge to Riker. Hold your fire!