The problem is that, in a country lacking a strong democratic tradition (i.e. Egypt), the democratic process is likely to be (and was being) subverted by whoever fills the power vacuum, in order to prevent ever being dislodged. The Muslim Brotherhood is radical and uncompromising. They were not interested in sharing power, nor are they interested in sharing it now that Morsi's government has been deposed. It's their way or the high way. Unfortunately, blocs that want power-sharing and compromise represent a minority of Egypt's fractious political allegiances.
It is difficult, to say the least, to have a country with a new democratic process actually stick with it long-term when such a form of government and civil society is not in their cultural DNA. It takes time to build that tradition to the point where you have stable, orderly transfers of power after elections. Look at the US: no matter how chaotic our election campaigns are, no matter how confused or bizarre, people do not end up taking to the streets to kill each other over them. At worst, we call upon the courts to resolve them and then live with that decision. We are invested in and believe in the process, even if we don't always like the results.
I'm not saying the coup (and it was a coup) was a good option. It may, however, have been the best of limited options. I suppose time will tell. You could argue that Egyptians should have waited until the Brotherhood outright canceled or rigged future elections before taking action, but then you and I are not the ones who have to live with the consequences of it, either way (unless you live in Egypt, in which case I apologize for speaking for you!)
It may be a long while before Egypt finds stability and reconciliation as they attempt to transition from one-party rule to plurality and compromise.