Did nobody tell parliament that Brexit was an issue? They've had 3 years to act. Why 2 more weeks is so critical isn't actually all that obvious in the big picture. If a 5-week break in parliament is the difference between outcomes in a 3 year process; it is too close to call and it is democratic enough whatever happens. The details are important but ultimately just politics.
On truly divisive 50-50 issues, either option is basically acceptable in a democratic country. Democracies are to avoid the 60-40 splits where countries barrel in to truly foolish ideas that nobody supports. Brexit or No Brexit by means fair and foul aren't going to be death blows; the public has been polled and the politicians have been given time to talk. Neither really expressed a clear direction. It falls to the executive to execute something.
Anyhow; courts made a good call. More talking makes for a happy parliament.
When you dont have agreement on what to do and a deadline is looming, it seems obvious that, however much it should NOT have been needed, it is in fact critical.
You arent chopping 5 weeks off of a 3 year period, you're chopping 5 weeks off of an 8 week period.
This is really about playing politics against Johnson and the government, not an actual outrage. Of course the government was doing the same by prorogating.
It's a pretty fundamental flaw that interferes with "near tossup means it could go either way" as a philosophy. It's a pathological case, but not uncommon.
Regardless of whether they could have acted sooner, Johnson's move was to prevent them from acting now when faced with a new administration and new course of action that had every appearance of going against both the will of parliament and (though less legally relevant) the will of the people in that most do not support crashing out without a deal.
You can't claim they had 3 years to act on the current situation when the current situation just arose in the form of a new PM that was attempting to side step any parliamentary review or legislation over his course of action.
Finally, they actually did act this past spring to vote that no deal wasn't an acceptable outcome. It was part of a series of non-binding votes that established governmental norms should have meant that it would be honored. When, after Johnson became PM, it was clear that it would not be honored, parliament quickly acted in the short time before being proroqued to actually enact in law the requirement to ask the EU for an extension in the face of no-deal. So, not only is 3 years not what they had to address the current situation, to they extent that they could address the current situation, they did so. Their desire to do more was prohibited by Johnson's (now illegal) actions.
Also length is a strong distinguishing factor. A few days or even a week or two are different enough in this situation to elevate a difference of degree to a difference in kind.
Finally, it happened with a PM that had a majority. Arguably the PM is not overuling the purpose of parliament when parliament itself agrees with the action. That is not the case here, there is no majority for the PM, and to all available evidence there is a majority that oppose this move by Johnson.