So, after a great deal of research, I ended up putting together this .reg file that would disable all the counters. Copy/paste this into a .reg file, run it, and reboot the server, and it will stop registering counters for commerce server
Windows Registry Editor Version 5.00
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\Commerce: Catalog\Performance]
"Disable Performance Counters"=dword:00000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\Commerce: Catalog Pipeline\Performance]
"Disable Performance Counters"=dword:00000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\Commerce: Marketing\Performance]
"Disable Performance Counters"=dword:00000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\Commerce: Orders\Performance]
"Disable Performance Counters"=dword:00000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\Commerce: Pipelines\Performance]
"Disable Performance Counters"=dword:00000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\Commerce: PromoCode Pipeline\Performance]
"Disable Performance Counters"=dword:00000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\csauthperf\Performance]
"Disable Performance Counters"=dword:00000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\cscustomperf\Performance]
"Disable Performance Counters"=dword:00000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\csdwperf\Performance]
"Disable Performance Counters"=dword:00000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\csmarketingperf\Performance]
"Disable Performance Counters"=dword:00000001
[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\csupmperf\Performance]
"Disable Performance Counters"=dword:00000001