The operations you are talking about, are "Window Manager" controls, which are not controlled by Tk. However Tk has a way to disable/enable them. Use overrideredirect(). In the code I posted above do this:

my $mw = MainWindow->new();
$mw->geometry("+100+100");
$mw->title("Main Window");

$mw->overrideredirect(1);

$mw->bind("<Return>", \&do_dialog);
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then if you desire to return full WindowManager controls back to the mainwindow, put:

$mw->overrideredirect(0);
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somewhere in your code where it's convenient, like only if you get a "yes" response.

You could also set it up to have your popup dialog use overrideredirect too.