if we start at the very beginning, zack’s first ingame mission initially acts like a true mission but resolves into a simulation. nevertheless, we do see the first hint of zack going ‘wait what, why do i have to do this’ and i like that we’re immediately shown that he’ll question shit he thinks isn’t right. he’s quick to notice that the troops he’s fighting are shinra troops and wants to know why they’re attacking him ( and it’s a lovely lil foreshadowing for Later In The Game ). angeal immediately tells him it’s fine, these are wutai troops disguised as shinra soldiers, and zack’s misgivings appear to dissolve. at this point in time, he is a fourteen-year-old second class soldier and things are really quite simple in his mind: shinra good — shinra road to heroics! wutai enemy, wutai bad. 

i do wanna note here that he doesn’t completely regard wutai as,,, yknow, evil or The Enemy, but it’s more that he. believes the shinra line about how they’re taking over this place to help them. shinra vc it’s fine guys, we’re just gonna rob this place and probably try to eradicate its culture but it’s To Help THem, we’re gonna give em resources and a mako plant or somethin! ( point is, zack thinks…. he thinks he’s Doing Right here. and that’s important. so long as he’s convinced he’s doing the right thing, he’ll stop questioning. )

note that he’s a ton happier to fight the behemoth toward the end of that mission. fighting monsters is so much less morally questionable. a lot of his early missions tend to end this way, with a nice big monster for him to take out so he doesn’t need to wonder if it’s right.

that leads us nicely to wutai and zack’s first mission with angeal. at this point, he’s buzzing. he’s just been suggested as a first class soldier. angeal’s with him. he finally gets to fight. he wants to impress lazard. he’s ready to kill without question here and it genuinely is a touch terrifying how eager he is. 

the wutai mission has that fun mechanic where you actually score higher the more enemies you choose to kill. there’s the option to walk away from them, to sneak through the fortress, but you get more points — more shinra prestige — for causing carnage. zack does not question this. he causes the carnage. 

except with yufi. she’s… she’s a kid ready to defend her home from him. i honestly wanted the game to give him a bigger reaction to that — my iteration of zack is certainly far more affected by this child, this self-professed hero, whose home is being invaded and who considers him the bad guy. he plays along, pretends to be beaten, but it’s the emotional impact that floors him, that makes him think ‘is this right and should i be questioning what i’m doing’. what is he accomplishing here, other than being part of destroying this kid’s people? it’s a scene that’s played lightly but is shockingly heartbreaking. 

he still does his part though. 

the scary thing is, if the whole angeal-genesis-sephiroth mess hadn’t happened, he might’ve continued that way. they’re the ones that make him begin to question — he hesitates initially to fight genesis’ soldiers because they’re shinra soldiers, they used to be allies — he fights them because they’re traitors and because he’s given reason to slot genesis nicely into the Villain portion of his brain and decide that means he’s in the wrong. 

i like to think zack’s declining faith in shinra has a direct correlation to how often he hesitates to follow commands. when it was angeal giving the orders, he was following someone he had trust and faith in. without that, the whole thing begins to feel empty and zack ( again, particularly my version ) is a fucking storm of a person who follows his own damn rules and his own beliefs.

zack lives for battle but he hesitates to take lives meaninglessly. he likes to consider his fights heroic, so long as he can convince himself he’s killing people to save other people. 

he actively Does Not Want to kill either genesis or angeal when ordered to. even with genesis, who’s killed people and is clearly going down a very dark path, zack hesitates. he’s just … like you said, processing. he wants to understand why this can’t be resolved without death — why there isn’t a better way. he fights only when it’s made plain to him that there’s no working around this. he’s told ‘kill’ and he’s like ‘okay but why’. ‘what exactly do you want me to do’. ‘w h y’. during genesis’ first supposed ‘death’, zack’s devastated. he didn’t want this. ( he actively makes damn sure genesis survives the next time. )

with angeal, he disobeys direct orders to kill. this is a breaking point of sorts for him, during which it becomes horribly plain to him that he is one of the few people here trying to avoid all this death. trying his damn hardest to reject those orders to kill angeal, only to do it anyway, results in a strange sort of shutdown in him. he doesn’t question anything for a while. fights because he’s told to. kills genesis copies. loses himself a little. he’s willing to kill hollander, where before his mind was set more on ‘capture and make him sort this shit out’. 

he says it himself: i’m soldier, so fighting’s all i do. he sounds scathing about it. disgusted with himself. he knows he’s a weapon to shinra and he’s letting himself be used, letting himself stop thinking because it’s easy to just follow commands and hope it all works out, because trying to do the right thing only wound up causing angeal’s death anyway. 

zack’s very much a person who wants to do right but gets a little confused along the way about what that is. a lot of his wariness in blindly following orders very much comes from his own strong moral compass, and the way the various influences around him seem to affect it.