Yes, there is a way to prevent this. You can add gui.applyHostDisplayScalingToGuest = "FALSE" to C:\ProgramData\VMware\VMware Workstation\settings.ini. Please see my post How can I disable a VM pref retroactively for more information on configure file locations.
I think enabling this pref by default in Workstation 12 was a bad move on the part of VMware. I have hundreds of snapshots taken and of course in them I've already set the display the way it should be. Every time I went back to a snapshot without that system-wide ban on scaling VMware tools in the guest changed the display settings. They should have done it differently. I understand why people might want this option but I have so many snapshots in the past it's easier to work without modifying them. Today is my first day with a system-wide ban and so far it's working as expected.