If you still have the windows partition that's preinstalled, skip the next paragraph.
If you don't, you'll need a windows partition or boot CD (BartPE might do it...though I haven't tested it without a windows partition, I dual boot). Download the "Configuration Utility" for the OS of your choice from http://www-307.ibm.com/pc/support/site.wss/MIGR-41987.html. Once you do this, run it, it'll extract an installation to a directory (by default C:\DRIVERS where Lenovo's stuff always goes by default). Go into this directory and run Setup.exe. This will install the ThinkPad Confriguration utility. Reboot.
Go into Start->ThinkVantage->Thinkpad Configuration. Click "Device Bay". Switch it to "Disabled". This will disable use of the docking station as well as acd0 with FreeBSD.
Dmesg will no longer see that ata bus.
Alternatively, if this is ABSOLUTELY not an option, since it appears to be related to acd0 locking up during initialization, if you're not using ultrabase you might also have luck with disabling the CD drivers in the kernel so it doesn't wait on that.
Thanks to Travis McArthur for the tip.Back to the X31 on FreeBSD page.