That's part of the problem: You don't need the PCs for your story. They seem to be more of a hindrance.
Let's not talk about realism, here. There are certain implied conventions in every RPG that have to be observed by players and GM.
Namely: The PCs are the protagonists, not the sidekicks and they trust that they have a chance to succeed. In exchange for that, the PCs take up the plot hooks of the GM without dismantling or questioning them too hard. You broke this agreement unilateral.
Some runs must fail is in no way acceptable. Because that just means you are taking away the PC's agency. You can make it hard, but you should give us the chance to recognize it as such. Point in fact: The guards being Prime Runners was in no way communicated or even hinted at.
Withholding essential Information is bad, bad, bad, bad, bad GMing.
You can certainly aim for gritty play, but you'll find that your players become very reluctant to do anything for your NPCs anymore.
About fast forwarding a few months: That won't solve anything. Instead it will force us to come up with ludicrous explanations why we stopped fighting when everything went to hell instead of leaving the city.
Finally, Kynos has In debt IV. He can't afford to sit on his hands because otherwise he loses his knee caps. That is another reason I am so pissed at being shafted again on the payoff of the mission.