I believe the safe way is first to understand perfectly how a metamod plugin works. To achieve this, download some simple plugins and look closely at their source code. I would recommend mine, since for each I try to keep the same structure (except the most complicated ones such as the bots). There are, basically, two interfaces in the HL engine, and metamod provides hooks for both. Once you get used to what these interfaces are, how they work and how to hook them, you can give a go porting your bot to metamod. Download one of the current metamod bot's source code and keep it as a reference on how to do things when you're really stuck.
And BTW, when your bot is a metamod plugin, you can compile it for Windows with MinGW32, or if you're a real geek do like Will Day and cross-compile it for Windows directly on your linux box
Anyway, thanks for the diffutils !