Can you back up 2 separate iPhones on a single PC using iTunes?

Yes, you can backup as many device as you wish. The backups themselves are tied to the device's individual unit ID and cannot be interchanged, even if you tried to do it.

As long as they each have a different name iTunes will keep the backups separate.

Yes you can (provided each device has a unique name)

Better still is to create a user account for each user on computer.