The flag button is not just the straight equivalent of the old Report button. Even the function of the Report button was often equivocated, there was some sort expectation that pressing it was tantamount to calling down a Low-Orbit Ion Cannon strike, whereas there were plenty of reports that didn’t result in any action, for a variety of reasons.
Generally, Discourse tends to encourage a self-moderating community, rather than relying solely on a moderator-centric approach, so users are both given an incentive and capability to resolve matters entirely on their own.
That also raises an interesting point, as I often noticed there were posts other users thought weren’t against the rules, where in fact, they were. Subsequently no report was generated, and otherwise unnoticed, these cases could easily slip under the radar. Over time this compounded, reinforcing the initial, erroneous belief that certain behaviors were allowed.
Finally, while it’s important to remember there is no outright censorship on opinions, certain opinions are more often than others expressed in ways that may be subject to moderation. There is being patently rude, and more subtly rude or inappropriate.
Most tend to focus more on the obvious, and have less clear-cut opinions on the latter cases. In doubt, it’s always good to ask.
My point is that ignore only works when there are definite sub-discussions which run parallel to each other with little or none overlapping or intertwining, which IMO is rarely the case in the threads where an ignore function is desired (and also the reason why splitting threads after the fact is often hard.)
When the software removes replies, too, is like putting on blinders that prevent the user from reading stuff they may find interesting, throwing away chances for a good sort of engagement.
BTW I have been working on reducing the scope of mega-threads, however, it’s not a switch you can flip overnight, but something that takes time for everybody to adjust to.
Finally, Discourse allows posting a reply as a linked topic: the function is documented in the Discourse Tips and Tricks pin, and it’s been used already, though I suppose you were away at the time.