Just found this topic. An interesting strain of conversation here I think, as a Mil ATCO with PPL I can certainly see both sides of the coin.
The one thing that springs to my mind about this from the ATCO perspective is the "fear factor". It's no secret that the junior controller cadre (me included) had the prospect of courts martial, negligence charges and the like thrown at us from week one of JATCC following several incidents over the last few years The phrase "get it on the tapes" particularly springs to mind. I think that there is definitely a culture in which controllers think they need to be seen to have done as much as possible so that if Joe Bloggs scrapes his Cessna 152 against Captain Smith's Dash 8 in Open FIR then the blame does not lie with the controller in subsequent Boards of Inquiry etc.
From the PPL side, I know that many junior and inexperienced PPL holders would not dare argue with instructions from ATC, even if they are not entirely sure of the reasons why. I dare say there is the potential for the GA aircraft put in an unsafe situation in order to protect the integrity of an IFR track to which the controller ultimately has greater responsibility. Controllers are not necessarily as aware of what the GA aircraft are trying to achieve and height restrictions are certainly part of this.