Everything is detailed in the Installation Instructions.
Yes, starting from FreeFEM-cs version 15, FreeFEM-cs and FreeFEM are kept in separate packages to allow everyone to pick the versions that they need.
Yes.
"Antoine Le Hyaric. Introduction to FreeFem++-cs. 2015. <hal-01169630>" (bibtex)
From version 11.14, when called with command-line option "-Batch" and a FreeFEM program file name, FreeFEM-cs automatically executes the FreeFEM program and returns control to the calling shell script when the program ends. FreeFEM-cs still needs to open windows, but this can also be hidden in Linux with xvfb.
To the best of our knowledge, FreeFEM-cs does not contain any virus or other security threat. The development machines are protected with a virus detector and they do not report any threat either. If your virus scanner reports otherwise, it is very likely a "false positive" (ie the scanner uses a "heuristic" algorithm that is not 100% reliable). Please check the suspected file through other scanners (see for instance the free online service http://www.virustotal.com) to get more information and let us know the result.