Well the unfortunate answer is MiniDLNA does not transcode and it is the only DLNA plugin for FreeNAS at this point in time.
You could add some software via the jail plugin but that is a nightmare and I don't know anyone who has gotten it to work. You also need a speedy CPU to perform the transcoding.
I see you have two fairly easy options: 1) Play the MKV files through a networked BluRay player (make sure it supports MKV, most do), or 2) install something like PS3Media Server or TVersity on a windows PC on your network and serve up your movies that way, neither one is my favorite software which is why I use option 1, the BluRay player that supports MKV. The third thing you could do is convert your MKV files into VOB files and play those through the PS3 but that takes a lot of time converting and is likely not what you want at all. I do have a fourth option, buy a TV that accepts MKV files via a wired network connection. I have that too but the picture quality is not as good as the BluRay Player.