This is an issue with curved (smoothed) paths vs straight line segments between the points, rather than with anti-aliasing.
In the ink tool (FreeHandCreate.cs in the PDFViewCtrlTools project) we distinguish between styluses and hand drawn ink, because on most devices (e.g. Surface Pro 2, Surface Pro 3), ink drawn with stylus looks a lot better if it is not smoothed. While ink drawn with the finger still looks a bit rough if you don't smooth it.
Basically, hand drawn ink is shown using a Bezier curve, while stylus drawn ink is shown using straight line segments.
In the FreeHandCreate tool, this is governed by the mIsStylus member variable. By setting it to false (or ensure it's not set to true) you can alter this behaviour.