Oh they were absolutely controversial and a frequent target of morality reformers.
By the late-1880s the column had devolved from the personal messages of the mid-century to consist largely of scams, guerilla advertising, and young ladies seeking the "assistance" of wealthy gentlemen (read: sugar daddies) and vice versa, often under the barely-there guise of seeking a husband.
A few ads abandoned discretion entirely...
By 1906 the Herald had become the target of an large-scale investigation by then-district attorney Henry L. Stimson, which was very publicly backed by William Randolph Hearst (whose participation I'm sure had nothing to do with that fact the The Herald was a large competitor).
The investigation, which included sting operations, concluded that "over two-thirds of the "personals" published have a hidden meaning which is harmful to the moral welfare of the community".
In the end the Herald was fined $31,000 for "improper use of the mails" - a favorite charge of morality crusaders used to prosecute the distribution of everything from erotica to information about contraception - and a much sanitized version of the personal column resulted.
(For the record, I personally didn't interpret the Mrs. JND/Manetta personal as an affair, but as two women attempting to buy property without their husband's knowledge - possibly in an attempt to escape and unhappy or abusive marriage. Though they could very well have been buying that property because they were madly in love with each other.)
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