Is there any preference or setting to prevent AFX from updating your workspace? If I have to open a rarely-used panel I don't want it included in my workspace profile the next time I open AFX.
You can create and save any custom workspace you want. I have 4. To find out how type Save Workspace in the search help files at the top right corner of AE.
To answer your question more specifically, no. You would have to reset the workspace before you close After Effects.