How to round the mesh that has a little complicated form? I tried to apply the bevel modifier to get a semicircle from the top of the rectangle but It worked only for a simple shape where the vertices between opposite corners weren't interrupted by other vertices. I can't join the 1, 2, 3 and 4 faces together either because the mesh is a little curved from the view from the top. So could you give me some advice?
You can use Proportional editing for this.  

Use you regular Move tool to move the vertices, and check Proportional editing.
Play with the falloff profile and size.  

You might also need to check Projected (2D) in your case.