Assassinate the Garbage Collectors
Every city has workers at the bottom, doing the nasty, dirty jobs needed to keep a city livable. Chances are, dear reader, you yourself don't 'see' these people in the places you live, yourself. These people run regular routes, serve everyone, and are likely to be amongst the least protected because they hold jobs people disrespect out of proportion to their need.
New York has roughly 9,250 sanitation workers for a population of 8.4M. We can assume, therefore, that our target city has ~5500 sanitation workers, all working at odd hours all over the city, likely without protection. Starting with the lowest-class areas, where police response will be the slowest, our commandos attack garbage routes, killing sanitation workers and disabling or destroying their equipment.
Even better, they generally don't have to be there to do it. Bombs can be placed in garbage, designed to explode at certain times, when being crushed by compactors, or when they detect they're being moved a certain amount (thrown in to the back of a garbage vehicle). This serves to both damage equipment and harm or kill the sanitation workers.
After the initial surge, hopefully decimating the sanitation workforce, psychological warfare can be played: garbage bags with 'I am a bomb' written on it. 'Tickers' set up inside trash cans that simply... tick. Or sometimes blow up. Or just go 'poof', scaring the bejeezus out of someone. Standard 'I am a Thirty Second Bomb' tactics targeted at sanitation - the key is to make it unpredictable, and sometimes deadly. After making it clear sanitation workers are under threat, and then making it unclear if at any moment they might be killed, the sanitation mechanism will grind to a halt. To hustle it along, the commandos can start to target sanitation leadership, removing the body of knowledge on how to best manage such a large scale of sanitation need, or make a splashy assault of a waste management facility, burning it to the ground and releasing a cloud of methane gas that takes weeks to clear out of the neighborhood.
Five million people produce a lot of trash. Dealing with a new reality where a non-critical critical piece of infrastructure is under attack, the rebels will have to divert significant resources to either protect this piece of infrastructure (thus not doing something else), allow the garbage to pile up (with associated health and morale concerns), or find a way to take out the commandos (assuming they're able to figure out that there are, in fact, commandos - this could be disguised). The sanitation workers would be in constant fear for their lives. It would be the sort of low-level chaos headache a rebel commander really wouldn't want to deal with.
And then you give the cows Mad Cow disease, or at least suggest the cows have it - or some similar thing. Any additional shock to the public understanding of their health and safety will make them deeply question whether the rebel leadership has their best interests at heart. This works doubly well if all such leadership are actually spared any direct attack. If the lower and middle classes are the ones under the primary stress, it will fracture their support from those at the top. In a few months, King Thin-Skinned will have a pretty easy time coming in and taking out the rebels. Once conquered, he has a ready-made, easy way to secure popularity: importing a bunch of extra sanitation workers to clean up the city and make it markedly better than it was under rebel hands.
Post Script: I don't know enough about main sewer lines, but again, there is a piece of critical infrastructure that is not 'critical' in the sense that it is guarded, and could be messed with. Not everywhere, but in enough places that you make things grody and unpleasant for the populace.