Here is my working code:
    /// <summary>
    /// Split PNG file into two JPGs (RGB and alpha)
    /// </summary>
    private void SplitPngFileIntoRGBandAplha(string imagePath)
    {
        try
        {
            // Open original bitmap
            var bitmap = new Bitmap(imagePath);
            // Rectangle 
            var rect = new Rectangle(0, 0, bitmap.Width, bitmap.Height);
            // Get RGB bitmap
            var bitmapInRgbFormat = bitmap.Clone(rect, PixelFormat.Format32bppRgb);
            // Read bitmap data
            BitmapData bmData = bitmap.LockBits(rect, ImageLockMode.ReadOnly, bitmap.PixelFormat);
            // Prepare alpha bitmap
            var alphaBitmap = new Bitmap(bmData.Width, bmData.Height, PixelFormat.Format32bppRgb);
            for (int y = 0; y <= bmData.Height -1; y++)
            {
                for (int x = 0; x <= bmData.Width -1; x++)
                {
                    Color PixelColor = Color.FromArgb(Marshal.ReadInt32(bmData.Scan0, (bmData.Stride * y) + (4 * x)));
                    if (PixelColor.A > 0 & PixelColor.A <= 255)
                    {
                        alphaBitmap.SetPixel(x, y, Color.FromArgb(PixelColor.A, PixelColor.A, PixelColor.A, PixelColor.A));
                    }
                    else
                    {
                        alphaBitmap.SetPixel(x, y, Color.FromArgb(0, 0, 0, 0));
                    }
                }
            }
            bitmap.UnlockBits(bmData);
            // Prepare JPG format
            ImageCodecInfo jgpEncoder = GetEncoder(ImageFormat.Jpeg);
            var encoder =  Encoder.Quality;
            var encoderParameters = new EncoderParameters(1);
            var encoderParameter = new EncoderParameter(encoder, 100L);
            encoderParameters.Param[0] = encoderParameter;
            // Save RGB bitmap
            bitmapInRgbFormat.Save(imagePath.Replace("png", "jpg"), jgpEncoder, encoderParameters);
            // Save Alpha bitmpa
            alphaBitmap.Save(imagePath.Replace(".png", "_alpha.jpg"), jgpEncoder, encoderParameters);
            bitmap.Dispose();
            bitmapInRgbFormat.Dispose();
            bitmap.Dispose();
            // Delete bitmap
            System.IO.File.Delete(imagePath);
        }
        catch(Exception e)
        {
             // Handle exception
        }
    }