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If your ultimate goal is to remove private agents when the next design refresh occurs...
...then your agent could just as well remove private agents straight away.
Apart from that I can confirm the behaviour you are describing. (Funny that I never stumbled across this before.) In fact, a design refresh will not remove private agents, even if the "P" in $Flags was removed. You have to remove also the "V", as mentioned in Barry's post. My best guess is that this is intended behaviour aiming at better protecting private design elements against design refresh/replace operations.
BTW, the FreeDatabaseDesign() function you are referring to, as it is, will effectively operate on any design element -- not just agents.
Feedback response number JSAK9MRC3U created by ~Chris Frofootherobu on 08/07/2014