Yes you can uninstall the unused instance and it is a good idea to do so. When you install SQL it installs a set of shared components and the SQL instance specific components. When you run the installer again choose the Remove option and it'll ask if you want to remove shared components or a specific instance. Select the instance you want to remove and then it'll give you the option to remove the particular features of the instance (DB, SSRS, etc). If you want to completely remove the instance then ensure all the features are selected for the instance (IIRC there is a button for that). It'll then remove the instance and related services but any remaining instances and the shared components will remain.
Note that it will not delete data files and whatnot so after the uninstall is complete you will still likely have some folders with the instance name in them. If you don't need them then you can remove them manually.