I'm guessing that you aren't aware that there are parasitic bacteria that currently live inside other cells. Since they are protected from the environment by their host it should not be difficult for them to lose the characteristics that enable them to be free living, pretty much in the way blind cave fish lost their eyes as they weren't necessary anymore and a waste of energy.

There is an arms race between viruses and their hosts. The virus wants to get in and reproduce and the host wants to protect itself. But as for virulence is concerned, viruses don't want to make their hosts sick or kill them. They want their host to stay healthy and protect and spread the virus so a low key virus that can infect a cell but doesn't cause much damage can be the most sucessful. The most deadly viruses for humans are those that jump from another species or which don't rely on healthy hosts to spread themselves. These viruses may be mild in the animals they usually infect, but humans lack the original animal's defences and so the virus can reproduce wildly. Over time new strains of the virus that aren't so deadly to humans can develop. (The same principle applies to bacteria and other disease organisms.)