That's a good question, and I would like to add my 2 cents in. How did the Orks not swarm the galaxy? I'll offer two perspectives on how Orks are kept under control. First I think there has always been a galactic hegemony to keep them in check. In the modern times, that is the Imperium. Then, there is local level defenses against the Orks, which will work against smaller hoards.
Hegemony:
I like to think that the Eldar Empire did not start off introverted; it just became that way as the Eldar society lost the need to work, and started delving more and more into self-satisfaction. For instance, we know the Eldar knew of Humanity; and considered attacking them; clearly, that shows the Eldar did care at least a little about the outside world. So, for the first millennium or 10 of the Orks existence, the Eldar battled them and kept them in check. We can add some more time because I imagine that the Orks were at first limited to a few sectors; it took a bit for them to spread to the point where they need culling.
So, we have the Eldar Empire starting off as the first galactic power working to keep the Orks in check. So, who takes the reigns as the Eldar go more and more insular? My guess is the first Human Empire. Remember that the Great Crusade was a reconquest of human territories as much as conquest of new ones. Since then, the Impeirum has gained more territory; but even halving Imperial controlled space gives us a huge chuck of the galaxy.
So, most likely, Golden Age Man kept the Orks in check as the Eldar introverted. IRRC, its been mentioned that Orks are humanity's oldest enemy. Then, of course, the Warp Storms blew in, Humanity's empire fell apart. My guess is that Warp-based travel was suspended throughout the galaxy and so the Orks didn't get to go much anywhere, either. Then the storms ended and the Imperium picked up where the Empire left off.
So, it seems to me that the galaxy has always had a major power that was at least in position to check the Ork's spread, so that should help keep the primitives and local powers safe. However, that hegemony can't be everywhere at once; local sectors would have to defend themselves. Since we really don't have much better info, I'll use the Tau as an example of a local sector and the Kroot as a primitive society.
Local Powers:
Most local species seem to have some sort of slow FTL travel, along with a navy and army. Most small sectors can deal with other local threats and defend their borders from pirates, raiders, ect. Otherwise, we have to assume that in this dangerous galaxy, the poor saps would not last long. So, defeating an Ork threat should be within the local empire's means. Of course, what size WAAAGH! the local power can handle depends on that local power's size, technology, and the Ork's WAAAGH!'s size.
The Tau Empire, for instance, seems capable of handling a small to medium sized WAAAGH! Some race with only three solar systems to call their own would most likely only be able to defend themselves against the smallest of WAAAGH!s and would be bowled over by the size of WAAAGH!s the Tau Empire can handle.
For primitive cultures, much the rules apply. If a hulk crashes with 50 Boys, and the local tribe or kingdom is on its toes, the primitive world should be ok. Again, that depends on the size of the WAAAGH!, local technology, and just how fierce the natives are. Kroot, apparently, did very well against the Orks when they invaded their home world. This is despite being not much beyond the Hunter-Gatherer stage of social advancement.
So, large WAAAGH!s have always been kept in check by the galactic hegemony. If an Ork threat is becoming very big, then the hegemony, whether the Eldar Empire, Human Empire, or Imperium will move in and cull the threat. Naturally, these empires are doing this for their own good, but their actions do save the small powers. The smaller WAAAGH!s left should be weak enough for the local powers to deal with.
So, in other words to answer your question:
But nowadays, the orks are EVERYWHERE, even with them Imperium to bash their heads in, how on earth did the primitive, pre-human civilizations of the galaxy even stand a chance against the seemingly uncontested rampage the orks could have executed?
I would think that the Orks took a bit of time to get started; to grow to such an extent that they became a galactic threat. Luckily, the Eldar Empire was there to keep them in check. Any WAAAGH! small enough to pass under the Eldar's radar would have been small enough that a local power could Handel the threat. If the local power couldn't, then the WAAAGH! grew until it was stepped on by the Eldar.