Direct current (DC) and radiofrequency (RF) plasma systems are similar in several parameters. You can use O2 plasma to increase the hydrofilicity of silk fibers surface or use an inert gas. Check the thermal stability of the natural fibers. You don´t need long periods of plasma treatment, however with high power and with the increase of time exposure the effect will be more aggressive.
The use of RF plasmas (13.56 MHz) using air is probably the easiest and least expensive process to modify the surfaces of silk fibers. Depending upon the power level and duration used, the surfaces will develop oxygen functionalities which render the surfaces more hydrophilic. In addition, depending upon the exposure duration, a microscopic roughness will begin to develop.
I fully agree to the comments of Emanuel and Bruce. Since silk absorbs higher amounts of water you can also try to use the desorbing water as plasma gas. This works very well with wool which adsorbs similar amounts of water during storage at ambient conditions. At the other side, when a special modification (e.g. plasma-induced hydrophobisation) is desired then you should try to remove most of the adsorbed water from the fibre by predrying.