If an epidemic sweeps through an alien civilization, reaching all corners of the planet, and is lethal to some percentage of the population, the main drivers of the civilization's progress are not affected. Population count is not a direct cause of technology progress, and it will continue after some delay caused by the epidemic. What is important to maintaining the progress is having a quorum of intelligent, problem-solving individuals who can organize their work to push the envelope of science forward, and then to apply it to the productive activities of the population. If there is some fraction of deaths, maybe even as high as 90%, this does not mean that the genetic resources that are needed to produce the future generations of scientists and engineers are lost, it means the numbers are reduced and progress will be slowed down, or even degraded for a period of time. But it does not mean a permanent halt, and the timeline for this society to be able to make star travel work might be delayed for a few generations.
To kill off the civilization as far as permanently eliminating their future progress, there would have to be a lethality level near to 100%, enough to eliminate so many of the population that there was a genetic reduction in intelligence. Is such a lethality level possible? Something lower than that might render the civilization incapable of maintaining its living standards, or even to preserve the existing level of technological know-how, but physical records and memories passed on to young aliens would lead them back to the standards they once had, and allow a resumption of the progress toward star travel.
Can an epidemic kill 100% of a population? This means that the contagion spreads world-wide, and that takes time, during which awareness of what is happening would travel all over the planet. Some response would be made, and the figure would drop below 100%. In the industrial era, when epidemics are possible because there is world-wide transportation and not yet rapid genetic developments of antidotes and antigens, there are still recourses to reduce the impact of the epidemic. Furthermore, with a wide mix of genetics for the immune systems, optimality having not yet been accomplished or even understood, there might be some aliens who are naturally immune, constituting some fraction of the population. And there might also be some individuals who are mostly resistant to the infectious organism's effects, recoving from it in more or less unimpaired condition. So, the achievement of 100% or very close to it lethality is unreasonable to suppose.
Before assuring ourselves of the recovery capability of a generic alien civilization, we might ask if there are any circumstances in which such a recovery might not happen. Regrowth needs resources, and if the civilization has already harvested the easy to gather ones, the minerals near the surface for example, could there be a barrier set up so that the civilization is bound down to a lower level of technology, one not capable of difficult extraction situations for critical items? Technological progess and resource development go hand in hand, and if the latter is impaired by what happened before the epidemic, could there be a strong barrier, sufficient so that the civilization would remain at some level, industrial or agricultural, forever?
This is a question related to the particular planet upon which the civilization resides. Does the planet have large, relative to the usage rate of the population, amounts of most necessary minerals and energy resources? Or is the planet, owing to where it developed and the history of supernova generation of heavier elements in the clouds nearby, rather short of resources? If the latter instance, could the near exhaustion of resources in the industrial era could leave the surviving civilization with only too-hard-to-obtain resources remaining? This means that, during this alien civilization's industrial era, no one noticed, or if it was noticed, no one responded to the problem, and the resources available to the civilization were rapidly diminishing and growing harder to locate and recover, and instead of the obvious solution toward reducing usage with a world-wide reuse plan, they simply continued to work toward an early resource exhaustion.
This does not make sense to rational people, but could there be some economic system which drove resource exhaustion heedlessly and recklessly. Could such an economic system stay in place when the costs of resources mounted steadily and significantly? This is an excellent question about the unbreakability of some economic systems. Can they be so firmly embedded in the culture that they would be blindly followed to near-term self-destruction of the civilization? Economic systems are in place because those who have the power to determine the ones to be used benefit from them, and so this question is, could these leaders of an alien civilization be only concerned with their own short-term benefits, and dismissive of what will happen to the civilization as a whole in only a few generations?
This question takes us further afield. Recall that the science of training children, which involves setting goals for them in the deep subconscious, may be completely unknown to the civilization, and child-training and goal-setting left to random choices by those responsible for that training. Thus, short-sighted goals might be preserved, generation to generation, including the goals that those who become leaders have. This particular realm of science is likely only able to arise in the later part of the industrial era, that of electonics and automation, or even in the early part of the genetics era.
There may be other mechanisms by which an epidemic could put an end to the future of an alien civilization, barring them from space travel, but this is one. It would only occur on a planet with less abundant resources, measured by how long they last during the industrial era, and only in situations where the neurology and training area of science happens to blossom late in this era. In this particular and possibly rare situation, a world-wide epidemic could have indirect effects that could collapse the civilization unrecoverably. But not only would these two requirements have to be in place, the epidemic itself would have to be at the limits of lethality, via both the disease effects and contagion. It might be that the evolution of such an infectious organism is extremely unlikely, and only by some early efforts at genetic engineering, at the level that would be possible in the later industrial era, could it arise and be, possibly accidentally, released.
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