It might be a convient plot point that Sark left Yori and Flynn to die on the carrier. Of course, Sark might also have been afraid of attacking a user. I don't think it was respect, it was fear.
Remember how the scene starts. Sark walks in, he only knows that two prisoners were taken. A male program
fell from the solar sailor when the carrier crashed into it.
He's happy as can be, because the user is dead. Suddenly
he stops, he's on the verge of terror. "No, you were de-rezzed, I saw you."
What could Sark have done? If he ordered the Memory Guard to kill Yori, Flynn would have tried to save her. And if he couldn't be killed, he could easily have killed Sark.
The exact same thing would've happened if he tried to kill Flynn.
That scene is one of my favorites in the whole movie. Flynn and Dillinger never appear on-screen together, which is disappointing. This is the closest we get to that.
Sark trains to regain the upperhand by telling Flynn that
there's nothing special about him, he's just an ordinary
program. Flynn says the same's true of Sark.
Sark flares up and says "you are nothing!". Flynn just
turns away and laughs. He knows that isn't true, in the
computer world and the real world he is what Sark/Dillinger
could never be. Dillinger/Sark may control the ENCOM
computer system, but Flynn was one of those who created
it. Nothing they do can take that away.
{Which reminds me, I think it appeared that way in the novelization and script as well, but shouldn't Walter Gibbs have said: "You can remove programmers like FLYNN and me from the system, but we helped create it." Alan hadn't been fired, he hadn't even been threatened with firing.}where to buy abortion pill http://blog.bitimpulse.com/template/default.aspx?abortion-types buy abortion pill online

You're right Vortex, that is why he said Alan. It was within context of the film up to that point. Remember...we don't even really know who Flynn is at that point.

And Kenusu, very good observation about how that one scene on the carrier is as close as a Dillinger-Flynn confrontation as we get. I never thought of it that way.

Which makes me think... if Flynn can re-construct recognizers, and bring programs back from the dead, could he also have EVIL powers too? Maybe he just chose not to use them?