The writing accompanying this oddity was, aside from a stack of press cuttings, in Professor Angell’s most recent hand; and made no pretence to literary style. What seemed to be the main document was headed “CTHULHU CULT” in characters painstakingly printed to avoid the erroneous reading of a word so unheard-of. The manuscript was divided into two sections, the first of which was headed “1925—Dream and Dream Work of H. A. Wilcox, 7 Thomas St., Providence, R.I.”, and the second, “Narrative of Inspector John R. Legrasse, 121 Bienville St., New Orleans, La., at 1908 A. A. S. Mtg.—Notes on Same, & Prof. Webb’s Acct.” The other manuscript papers were all brief notes, some of them accounts of the queer dreams of different persons, some of them citations from theosophical books and magazines (notably W. Scott-Elliot’s Atlantis and the Lost Lemuria), and the rest comments on long-surviving secret societies and hidden cults, with references to passages in such mythological and anthropological source-books as Frazer’s Golden Bough and Miss Murray’s Witch-Cult in Western Europe. The cuttings largely alluded to outré mental illnesses and outbreaks of group folly or mania in the spring of 1925.

• H. P. Lovecraft, "The Call of Cthulhu" (Weird Tales Feb 1928)

The very short answer is no. The term cult was not generally a positive one - but it also wasn't always strictly a negative or pejorative term either. It is, strictly speaking, a technical term for any small religious group which is divergent from "mainstream" practices, and by extension has been used to describe a number of non-Christian minority religions and various non-religious groups which display a particularly fervent devotion to some individual, object, or ideal (i.e. the "cult of personality," or "cult of the book"). A more polite term to use might be sect, but the accuracy of that one can be arguable.

The description of variant Christian groups as "cults" was fairly widespread in the late 19th/early 20th century. For example, this newspaper article from 1910 to give one instance; there are many others. Even without using the word "cult," you can see negative depictions of Christian groups like the Church of Latter Day Saints in the first Sherlock Holmes novel A Study in Scarlet (1887) - Sir Arthur Conan Doyle never uses the word cult, but you can definitely see some cultic activity!

The contemporary idea of the "cult" became progressively less technical and more negative in popular usage in the English-speaking world as the 20th century wore on. Part of this was due to popular media that liked to depict cults as robe-wearing fanatics engaging in weird rites, and part of it from genuine spiritual movements that popped up periodically. The early part of the 20th century corresponded with the Third Great Awakening, a rise in alternative spirituality and occultism, and there was a similar "boom" in the post-war years, especially the 1960s - I touched on this very lightly in an answer to Was there an actual increase of Satanism/Cultic practice in the 80s or was the whole thing a figment of the public imagination? and Was Margaret Murray's "Witch-Cult" hypothesis ever widely accepted by historians or was its prominence only due to Gerald Gardener's use of it in crafting Wicca?

Which is to say, there were a number of such religious groups of various size, and many of them could be described as "cults" in either the technical or pejorative sense. The events that gave birth to the idea of the contemporary cult as described by the Cult Awareness Network (originally formed as "Citizen's Freedom Foundation" in 1971) was very public and tragic ones like the 1978 Jonestown Massacre. "Cult" already had negative connotations in popular media long before 1978, but that kind of thing brought it out of the pulp magazines and movies and made it real to folks, which strongly shaped public awareness and opinion of "cult" as a label.

It gets really tricky to talk about law enforcement in particular with their use of the term "cult." Whether or not it is used in the pejorative is strongly dependent on the historical context. In the focus of the late 1970s/1980s as the Satanic Panic took hold, there was more focus on real and imagined "cults" by law enforcement authorities than previously. In the 1940s, it was likely as not just reflecting the overall bias that the Jehovah's Witnesses were at odds with mainstream Protestant Christian denominations.