AVISynth will be slow no matter what, and it only gets worse when you have a high cpu codec like h.264 inside your mkv. You have two options to speed up your editing:
1) Figure out what clips you need, then use VirtualDub to convert them to AVI files with low-overhead frame-accurate codecs such as Lagarith, HuffYUV, or MJPEG.
2) Remux the entire MKV as an MP4 file. Use mkvextract (part of mkvtoolnix, GUI available separately, just google for mkvextract gui) to get the elementary streams (yourvideo.h264 and yourvideo.aac or whatever) and then use the MP4 Muxer in MeGUI to remux those into a MP4 file that's directly compatible with Premiere.
Also, I second the inserting of the normal comment about using DVDs. (Most) H.264 files are not frame accurate. If I have to have the 1080 or 720p version, I use Premiere to timeline, then figure out what cuts I need, virtualdub the cuts to Lagarith, then replace the footage in the timeline.