Update one instance of Sql Server 2008 R2 Standard to SP2?
Yes, you can choose which instance(s) you wish to apply the service pack. They'll all be checked by default; as will the client tools / shared features (there is only one "instance" of those):


  


You can re-run the installer later to update any that you didn't update this time; the ones that are already at SP2 will not be selectable.

On this VM, I have 2008 R2 RTM (no patches whatsoever) and 2008 R2 with Service Pack 2 and CU9, installed and running side by side with no issues:


  


Now, why you want to have a mix of patched and unpatched instances on a single server might be a different question...