Dynamically importing and processing content at runtime is explained in the sample WinForms Series 2: Content Loading. This is the preferred method.
You can also build an XNA Content Project file using MSBuild. this blog post explains how. You can create a temporary project file, so you don't need to modify or rebuild files in your Solution.
Additional information in this blog post. It helpfully explains the layers of the XNA Content Pipeline (so you can decide what layers it would be best to interface with to meet your requirements).
