Have you tried machine=vgaonly and cputype=386 (given these are in unpatched builds).
Have you observed lower framerates when WC1 slows down? Could you verify with FRAPS or similar, if possible? If the slowdowns are associated with the frame rate, then it may be possible to run the cycles at that higher end (~9000) rate and then "clamp down" on the cycle speed when the video is updating too frequently. There must be many parts of the code where this can be attempted.
Edit: attached a binary for testing with Wing Commander 1 and 2; it is SVN code with a feature active to "keep VGA changes". I presume this will slowdown the emulation and change the way the screen updates. It also doesn't work with EF2000, for instance, but the older Doom2 is functional. However, I have no test case, so it may be worthwhile to test the binary with WC1.
Meanwhile, I wonder whether a frame limiter could be enabled by a variable in the Normal_Loop and a global variable which stores the frame rate in the video emulation.
Edit 2: Hal has a dosbox build with memory slowdown here: Re: game speed is not constant ; I would test it against WC1.