The Protheans lasted a long while against them. And that darken the skies quote came from an arrogant reaper that was overstating and flat out lying about their power. No beginning and infinite. They aren't gods. Even the loss of one reaper would be unacceptable unless there is a backup system in place, which I think is likely.
The protheans lasted a long time because the reapers allowed them to last a long time. The reapers took their time in the harvest. They isolated the protheans, they cut them off from one another. They were each stranded in their individual systems. Also there is no reason to think the reaper was lying about its numbers. If you took ALL the reaper ships and put then over the world it very likely would darken the skies. They have a huge number of ships do not be fooled by Mass Effect 3. Remember that the situation in the Mass Effect cycle is vastly different from other cycles. The reaper's usual plan of attack is to take over the citadel and cut us all off and leave us stranded. They systematically harvest us system-y-system. In ME3 they're scattered out everywhere. This is very different from how they usually handle things.
I had an interesting conversation with Vazgen about the 'reaper backup' concept which I will share part of it here.
"The reapers harvest us, turn us into goo and pump us into giant reaper forms. If they can just make a digital backup copy of all this and store it someplace else it makes me question why they bother going through all that effort in the first place for the original copy. What importance is it to store our genetic material and make organic-synthetic reapers if the knowledge that organic paste allegedly holds is something that can be stored like normal data? Reapers would not have to be part organic, they could just copy the data from the organic stuff and port it over to full-synthetic bodies.
See my biggest issue with reapers just being backed up is the fact that they're partly organic. That organic bit is important, it represents the harvested species used to create the reaper. When a reaper is destroyed this organic matter is lost. If everything a reaper was can just be uploaded to pure hardware then it takes away the significance of that organic material. Which makes this less 'harvesting' and 'preserving' us and more just archiving our knowledge."
We did come to a rather satisfying compromise, imo.
"How about a compromise between the two beliefs that might work well together? The harvested maintain a sense of awareness, all those minds linking together to form one. For this to happen the organic paste has to be kept 'alive' as it is the very essence of the species that make up the reaper. Able to come up with new ideas, to think and live. However if it dies the memories and knowledge that it had are saved to catalyst. So while it will maintain all the knowledge it knew, the 'life' is gone forever because the organic material that gave it life is no longer there. It goes from being a sentient reaper to being just information."
I certainly don't expect many to share this perspective, though. Too many people are too emotionally-driven and refuse to view the reapers as anything more than giant killing machines. Lol.