Introversion

SPOILERS

I wondered what would happen if you jailed the top agent before he would "commit suicide".

I hacked the Uplink ISS
Stole the agent data and decrypted it
Hacked the GCD and had the top agent arrested

To my dismay it didn't actually change anything. The story still progresses as usual, with voiced concerns from no.2 and then reassurance from "no.1", leading to his death.

i noticed discrepancies like this too (MORE SPOILERS):

i jailed the top agent after he had already committed suicide. news article had no mention that he was already dead =P.

I jailed all the agents.. then i gave away the user data and they started being killed - ok maybe they can catch them in jail but it seemed like that wasn't taken into account.

Yeah, the game does not take into account what the agent is doing, so it is entirely possible to kill an in prison agent, or in one case arrest a dead one. It happens and its just part of the game, roll with it, it happens.

The worst discrepancy is your own existence in Uplink. Seriously, look into that one.

What do you mean by "giving away" the user data? Where do you publish it? I know I can tamper with all their files, but how do you get them killed?

steal it and wait, you will find out.