Can you copy the xml and delete the references? No. You have to look at the references in the beginning, see what the alias is, then you would have to go through the xml and delete out the sections applying to the alias given by the reference.. so for example:
Windows.Computer is a class right. If you see this class in SCOM in XML, it might look like this: Windows!Windows.Computer (the Windows part of "Windows!" is the alias for the discovery management pack, that is referenced in your mp. If you look at references for "Windows", at the top of the XML, you will see a full mp name that is correlated to that reference.
Having said that, I think someone made a tool or a script, that would go in and strip your mp of bad aliases. But this is not the case in your situation, at least I don't believe it is.
SystemCenter Advisor is a default installed mp, and can be removed unless you use Advisor. App monitoring 360 sla, I believe that is a default mp, but can also be deleted. Network discovery, default mp, might want to keep that. Notifications contains all your notifications, do not modify that.