What people usually forget when studying history is understand the difference the moderrn prespective on matters and ancient time's. Alot of times people commenting on historical events forget the importance of "prespective" and without knowing they make commentso n events based on a modern prespective that didn't apply in the said era they have been speaking about.
In this case speaking about if Zhuge Liang was feared or not historiclly, before being able to answer this question you have to look back on prespective on life, human character and world events of the three kingdoms era. Back in the ancient days people still somewhat believed in "magic" in "imortality", they believed in "spells of gods" and all that stuff. Reason behind it was due to the lack of realible news and information being passed down. There wasn't a news network back then, no televised events, no detailed pictures, only thing that people would know about someone else in a far off land was through word of mouth. Generally druing the era of three kingdoms men looked at each other from a different prespective then they do today. Men weren't "equal", example of that would be the emperor who was known to be "son of heaven" and people really did "fear" and "respect" the son of heaven's powers and wishes. People really believed that certain humans were above others, so being the prespective of people.
If someone takes into consideration the people's behaviour, belifs and prespective on human status and equality druing the era of three kingdoms, he would be able to better understand personality images of ancient characters.
So in my opinion, yes Zhuge Liang was feared by his enemies, some may have belived that he could really control powers of heaven and earth, his reputation were from word of mouth and over exagration of his acomplishments, and these over exagrations often let people to belive them as "superhuman powers" due to lack of science and general knowledge back then. It was very common for common men to view higher status humans as people with "super powers" and such prespective wasn't just in china, it has been all over the world in different nations and civilizaitons. such as the persian kings, the islamic leaders, japanese warlords.
In conclusion based on my humble opinion, yes Zhuge Liang was known as a man with super natural ability and generally feared through out china.