A little messy but this should work i think. Basically controls are stacked. So having the grid come after the first grid it shouldn't effect the opacity. May need to be tweaked, but something along the lines of this should work:
<Grid Grid.ColumnSpan="2" Grid.RowSpan="2" Visibility="{Binding Alertar, Converter={cnv:boolToVisibilityConverter}}">
<Grid.RowDefinitions>
<RowDefinition Height="2*"></RowDefinition>
<RowDefinition Height="5*"></RowDefinition>
<RowDefinition Height="2*"></RowDefinition>
</Grid.RowDefinitions>
<Grid Grid.RowSpan="3" Background="Black" Opacity="0.5" />
<Grid Grid.Row="1" Background="Black" Opacity="1">
<Grid.ColumnDefinitions>
<ColumnDefinition Width="3*"/>
<ColumnDefinition Width="7*"/>
<ColumnDefinition Width="3*"/>
</Grid.ColumnDefinitions>
<Grid.RowDefinitions>
<RowDefinition Height="10*"/>
<RowDefinition Height="1.5*"/>
</Grid.RowDefinitions>
<Rectangle Grid.ColumnSpan="3" Grid.RowSpan="2" Fill="Black" Opacity="1"/>
<TextBlock Grid.Column="1" Margin="0,15,0,0" Text="{Binding ReporteInconsistencias}" />
<Button Grid.Column="1" Grid.Row="1" Content="Aceptar" HorizontalAlignment="Stretch" VerticalAlignment="Stretch" Margin="10"/>
</Grid>
</Grid>