Admittedly I haven't read the book myself, but I've often thought about this (and other situations like it) so here is my two cents.
Hive Cities do not normally manufacture weapons. At least to my knowledge, but maybe this one does. Hive Cities are a form of control on the populace as a whole. It is much easier to control people when they're forced to live inside of the hellish hive you've built for them, than if they were scattered in numerous cities (of similar sizes as our own). Controlling that many people would be hellish on an authoritarian system like the Imperium. Hive Gangers certainly would get their hands on weapons but these would likely revolve around the stubber variety with a relative handful getting a hold of more advanced technology such as lasguns, laspistols, and maybe the leader has a bolt pistol or something.
I'm not certain either that the average Imperial citizen in a Hive, no matter how wretched that place is, would be tougher than another other Imperial citizen or indeed even anyone today. Hive Worlds are also formed by necessity, often times massive over-industrialization, rampant pollution, and ecological meltdown have forced the hand of the planet to consolidate into Hives. This means that while the planet can usually sustain life, its often not a very high quality of life. This probably wouldn't effect the Upper Hivers since they would be the ruling class and would have better access to medical care, or probably just have filters in their spires. The average Imperial citizen is probably weaker than an average person today, they likely have a lower IQ (since authoritarian regimes do not usually like intelligent subjects -- see Tsarist Russia), and are generally unhappy with their lot.
In my opinion the above reasons would give me the impression that the Orks would have a major upper hand against Imperial citizens -- no matter how many of them were thrown at the Orks. It is believed that the boltgun was designed specifically with the Ork in mind since it usually takes a few bolt rounds to the chest to actually kill an Ork -- results may vary obviously. Stubber guns would have to unload a simply massive amount of ammunition into the Orks to break them. Orks are tougher than humans in general and I beleive probably even tougher than Hivers. Let us even assume that the Gangers are tougher than bricks, have weapons, and actually WANT to fight for their tyrannical upper hiver lords -- they still would not stand up to a organized (by Ork standards) assault.
To comment on your second point -- the complexity of Hive invasions. All of that is a good point. Hive Cities would be downright nightmares to try and navigate through -- most of them were originally well-designed but over successive generations of incompetent leadership are probably very ad-hoc structures that could likely (and probably do) collapse in on themselves regularly. In this case I believe the Orks would be banking on their sheer terror-factor. Normal humans are written into the Warhammer 40k universe as the very bottom of the food chain or close to it. Orks rampaging through your Hive city would be pretty terrifying and would make any kind of coherent, military-styled defense almost impossible. Once command and communication broke down it wouldn't take long for the Orks to simply divide the defenders and cut them to pieces. This is especially true if these militia are really Hivers who've been thrown guns and put into some ad-hoc system of command under the PDF. You can imagine this being even harder with Gangers involved as they simply don't follow orders.
The last point of the Levels -- another good one. I think the point is, if they took that first (I'm assuming its the level on elevation with the natural ground of the planet) level, I imagine they wouldn't necessary need to take any other level. They've broken the logistics chain from the upper and lower levels, and from the planet at large. There is a possibly that the Upper Hivers could have food imported by air -- but most planets probably don't have the planes and material to do this. So for the Orks, assuming they don't just go all Orky and randomly invade stuff, can just sit back and starve the Hivers out, forcing them to make suicidal assaults to try and break out. Hive Worlds are notoriously dependent upon food imports, as their populations FAR exceed their domestic food production.
That is my two cents. Hope it helps to shed some new perspective on the matter.