If you're using the default built-in AD OU structure, then chances are you've not implemented anything that would be affected by changing OU membership, therefore the answer is likely "Yes, you can change your workstations OU membership without affecting anything."
No do not touch the built in Domain Controllers OU, nor touch any of the servers listed in there. We'll get back to this later.
And one note -- I don't think you're using Small Business Server, but if you are, or for the benefit of other readers that may come accross this post, don't change the OU structure of SBS.
FOr your case, I suggest the following:
1) Download and install the Group Policy Management Tool (GPMT).
2) Create an OU for "Workstations" and one for "MemberServers" for example. For ease of organization, you can nest these inside of a parent OU called CompanyNameOU (I also create OU's for Users and Groups under my CompanyNameOU).
3) Change your Workstations and Member Servers OU membership accordingly
4) return your Default Domain GPO to its original state
5) With GPMT, create a new GPO linked to your new Workstations OU, adding the desired workstation WSUS settings to this GPO
6) Create a new GPO linked to your new MemberServersOU, adding the desired MemberServers WSUS settings (maybe you want these to install updates only once a week rather than daily for example)
7) if applicable, link the GPO created in Step 6 above, to the built in Domain Controllers OU
last note, in the OU's created above, since you're only implementing settings under Computer Configuration, I will typically disable the User Configuration section of the GPO -- no need to process that section if you know it's empty.
As far as expected issues? None, unless you consider organization and structure, an issue.
