Downloaded the WC pack in the summer sale and I had this exact same problem. This is the first thread I found when I searched for a solution, so time for an epic year later bump. WITH A SOLUTION! One I honed in on myself.

This fix means tinkering with the dosboxWC.conf file (located in Drive [D]:\GOG Games\Wing Commander 1 and 2\WC\". Keep in mind your results may vary, as DOSBox's speeds are fairly dependent on the system it's running on.

Change these settings as follows:

fullresolution=0x0
output=ddraw

machine=vgaonly
memsize=2

frameskip=0
aspect=true
scaler=hq3x

core=normal
cputype=386_prefetch
cycles=fixed 3000
cycleup=100
cycledown=100

Also a side note: Using a joystick seems to affect the game's speed as well. I actually had to LOWER the cycles from 4400 after hooking one up.