Perhaps, if you use function set() instead of image(), you may get an opaque result.

When you use bitshifting and the pixel array directly, it doesn't seem to greatly impact the fps.

Code Example

1. // Tested with Processing 2.0b8
2. 
   
3. PGraphics pg;
4.  
5. void setup() {
6.   size(500, 500, P2D);
7.   pg = createGraphics(width, height, P2D);
8.   pg.beginDraw();
9.   pg.smooth(4);
10.   pg.noStroke();
11.   pg.endDraw();
12.   noStroke();
13.   fill(0, 255, 0);
14. }
15.  
16. void draw() {
17.   background(255); // white background
18.   rect(0, 175, width, 150); // green rectangle
19.   drawPG();
20.   if (mousePressed) ignoreAlpha(pg);
21.   image(pg, 0, 0);
22.   frame.setTitle(int(frameRate) + " fps");
23. }
24.  
25. void drawPG() {
26.   pg.beginDraw();
27.   pg.background(255, 0); // white 'invisible' background (also works with opaque white)
    
28.   pg.fill(255, 0, 0); // red opaque ellipse
29.   pg.ellipse(pg.width/2, pg.height/2, 250, 250);
30.   pg.fill(0, 0, 255, 125); // blue transparent ellipse
31.   pg.ellipse(mouseX, mouseY, 200, 200);
32.   pg.endDraw();
33. }
34.  
35. void ignoreAlpha(PGraphics pg) {
36.   pg.beginDraw();
37.   pg.loadPixels();
38.   for (int i=0; i<pg.pixels.length; i++) {
39.     color argb = pg.pixels[i];
40.     int a = (argb >> 24) & 0xFF;
41.     if (a!=255) {
42.       int r = (argb >> 16) & 0xFF;
43.       int g = (argb >> 8) & 0xFF;
44.       int b = argb & 0xFF;
45.       pg.pixels[i] = 255<<24 | r<<16 | g<<8 | b;
46.     }
47.   }
48.   pg.updatePixels();
49.   pg.endDraw();
50. }

Thanks GoToLoop, amnon.owed. both your solutions do the job. Since I was looking for a GPU solution to avoid using loadPixels, I came up with the following shader which does what I need to the frameBuffer I am using. It also works fine with sending the frameBuffer via Syphon to another application, here the code I use (the shader is at the bottom of the sketch):