Your second example is writing an eps file. When you write to a stream the Format of the input stream is used. If you want to write to a different format you will have to set the Format property of your MagickImage.
using (MagickImage image2 = new MagickImage("fileSource.eps")) { image2.Strip(); // This uses the format of the input image.using (Stream fs = new FileStream("thisIsActualyAn.eps", FileMode.OpenOrCreate)) { image2.Write(fs); } image2.Format = MagickFormat.Jpeg; using (Stream fs = new FileStream("fileDestination.jpg", FileMode.OpenOrCreate)) { image2.Write(fs); } }