If you have the resources to dedicate a complete server for ABP for 50 clients then sure, put it on its own server
if you dont have the resources i suggest you put the ABP software on a server which has no (critical) IIS services running. I myself will put the software on my fileserver, since basicly what it does is serving files (and my disks are configureed for that need).
You can start an uninstall job from the ADNM if you want.
You can also deploy the ABP client over the adnm netclient.
If you really enjoy uninstalling manually (which actually is the safest way to go) then use the special uninstallation tool for removing the client.
You can uninstall all clients
Remove the old ADNM installion
Depending on which SQL database you use, you should remove the old instance and install a new instance with windows authentication