there was a real debate about whether the idea for the mass extermination of jews came directly from Hitler (or whether it came from the lower level bureaucrats)

This isn't a great understanding of the intentionalist-functionalist debate. The I-F debate is over whether the upper ranks of the Nazi party intended to exterminate all the Jews they could get their hands on from the beginning or whether the idea became more attractive because of various other factors like setbacks in the war. For example, functionalists often point to the fact that there was a plan floating around to set up a "Jewish colony" in Madagascar to which they could deport all the European Jews. The failure to defeat the British made this impossible. On the other hand, the einsatzgruppen on the eastern front were assigned their bloody task when Germany was clearly winning the war. I have the feeling that the answer, just like every other binary postulation, is that both positions have some truth to them, but intentionalism is more true.

So, for your original query: yes, it is a legitimate academic debate; no, it is not a form of Holocaust denial.